Short Circuit only when the Main Breaker is OFF

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I recently wired a portable generator on a older style 200A Square D Homeline panel with a mechanical interlock bracket. When I shut the main breaker off to run power of the generator, the breaker on the portable generator kept shorting out. I started troubleshooting and found that over 20 branch circuits were shorted out but only when the main breaker was in the off position. Is there any reason why this is occurring or would this be from multiple wiring issues?
 
How are you hooking into gen, power cord on the 30A 4 wire, and gen receptacle?, or another means? First instinct would be check connections from gen, reversal of neutral hot or hot ground. Wiring error on generator from factory to plug assembly. Test gen without connection to house loades, does it hold then, test cordage and plugs ability to hold without house load.
 
When I shut the main breaker off to run power of the generator, the breaker on the portable generator kept shorting out. I started troubleshooting and found that over 20 branch circuits were shorted out but only when the main breaker was in the off position.
How do you determine that "over 20 branch circuits were shorted out"? If just reading from hot to neutral/ground they could be circuits with a load that you were reading through.
 
Better check your wiring from the generator to the panel. If the panel running off Utility works fine then you either have it wired wrong or there is mis-wiring in the generator. If you had 20 circuits shorted then it wouldn't run on Utility.
 
... First instinct would be check connections from gen, reversal of neutral hot or hot ground. Wiring error on generator from factory to plug assembly. Test gen without connection to house loades, does it hold then, test cordage and plugs ability to hold without house load.
How do you determine that "over 20 branch circuits were shorted out"? If just reading from hot to neutral/ground they could be circuits with a load that you were reading through.

Agree on these comments.
Were the 20 branch circuits all on the same phase? If so then that might point to a reversed connection of that phase with neutral or ground like Fred B mentioned above.
 
Does the generator have GFCI protection?
I didn’t check if it does, but my issue is at the panel strictly. I isolated the panel away from the generator and my problem is when the main breaker is off there’s continuity from the bust bar to ground therefore when I back feed the panel there’s a short circut
 
As long as there are loads connected and turned on, including transformer primaries, you will get very good continuity between hot bus and neutral with the main breaker off. With the main breaker on you cannot attach an ohmmeter!
If you open all branch breakers does the generator still trip off and do you still get continuity from hot to neutral?
Remote possibility of a mechanical short inside main breaker, but it should not have any neutral connection in the first place.
 
There was a short with a load on but it’s a Siemens panel which is now homeline and definitely older so I think it’s a good possibility of it being a faulty main breaker. Would that mechanical issue cause a short on some but not all circuits?
 
Need much more info. Though most likely incorrectly wiring on the generator side. Anything from cord wired wrong, to inlet wired wrong. First step is to check voltage at each point.
 
Need much more info. Though most likely incorrectly wiring on the generator side. Anything from cord wired wrong, to inlet wired wrong. First step is to check voltage at each point.
When I was troubleshooting I eliminated the generator from the panel by shutting the 2 pole 30A breaker and notice that when the main breaker is in the off position there a short on multiple branch circuits. I think it’s either a wiring issue in the house or possible a bad breaker. It’s strange but it seems to be a problem they would have never discovered until I tried to back feed the panel with a generator
 
When I was troubleshooting I eliminated the generator from the panel by shutting the 2 pole 30A breaker and notice that when the main breaker is in the off position there a short on multiple branch circuits. I think it’s either a wiring issue in the house or possible a bad breaker. It’s strange but it seems to be a problem they would have never discovered until I tried to back feed the panel with a generator
Please tell us exactly what you are measuring and with what equipment, when you say "short". Are you seeing branch "shorts" with the branch breakers open? If so you can also measure with branch breaker open and main closed. The one thing the generator connection might provide is a solid connection between EGC and neutral.
Do you get the same measurements with the generator cord disconnected from the inlet.

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Stop calling them shorts unless you can clarify what your ohm readings are. As others have mentioned, if you are just measuring continuity through loads then by definition those are not short circuits and not the problem.
 
When I was troubleshooting I eliminated the generator from the panel by shutting the 2 pole 30A breaker and notice that when the main breaker is in the off position there a short on multiple branch circuits. I think it’s either a wiring issue in the house or possible a bad breaker. It’s strange but it seems to be a problem they would have never discovered until I tried to back feed the panel with a generator

Your measuring continuity.

All that means is there is a continuous path for the electrical circuit to flow.
A light bulb has continuity, not a short
 
Please tell us exactly what you are measuring and with what equipment, when you say "short". Are you seeing branch "shorts" with the branch breakers open? If so you can also measure with branch breaker open and main closed. The one thing the generator connection might provide is a solid connection between EGC and neutral.
Do you get the same measurements with the generator cord disconnected from the inlet.

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I was measuring ohms with my fluke meter between the panel ground and the branch circuit screws in the on position. I don’t have an exact measurement for ohms but I went through the entire panel and the 20 circuits that did not have continuity I left in the on position and ran the house off the generator with above half the circuits on and the ones with a short I left in the on position. Also it was not evenly distributed as for what circuits work and didn’t work it varies between the two legs
 
Is your generator 120/240 volt or are you trying to feed the same 120 to both L1 and L2 buses? Have you calculated the loads which you have connected to the panel and compared it to the output rating of the generator? Allowing for inrush on motor and transformer loads? Saying that the "breaker on the generator shorted out" is totally inappropriate. The breaker is opening, not shorting out. I will do that when the load is too high, but not so high that it stops the engine of the generator.

As noted by others, if you have, for example, a light bulb on Branch A, then with Breaker A open you will measure the cold filament resistance of the light bulb between branch hot and neutral. The cold resistance of the bulb can be a little as 1/10 of the operating resistance.
 
Again, you're not reading shorts, just normal loads. The breakers that don't show continuity happen to have all loads turned off.

Try turning OFF every breaker, then try it. If it still trips, then whatever is tripping is most likely GFCI-equipped.

If it doesn't trip, then turn on one breaker at a time, starting with only single-pole breakers.
 
Try thinking about this in the most simple way. It could be a design thing.
It's possible that the mechanical interlock not only has provisions to lock out the breaker from closing
but also intentionally shorts out the load side of the breaker for personnel safety reasons. Kind of like the same way
a shorting truck works when racked into MV switchgear.
If this is the case then it may be possible to modify the interlock and remove the shorting device linkage.
 
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