All breakers are off leaving ground and neutral connected somewhere on the boat tripping pedestal. The isolation transformer eliminated that, but you still have the two connected somewhere. Inverter or main panel buss bars?
Should it be left that way?
The tripping breaker was the symptom, not the root problem. And adding an isolation transformer, though a good thing all around, has simply covered up the root problem.
With the iso transformer in place, you still need the onboard neutral and ground bonded at all times, and bonded in one and only one place. There are basically two ways to do this.
1) Bond at each power source, and make sure that each source's bonding only carries through to the rest of the boat when that power source is selected. This is probably the most common approach, but you really need to think it through carefully, one power source at a time, to be sure you are always bonded when using that power source, and not double bonded when using another power source. Inverter/chargers can be tricky because sometimes they are power sources, and sometimes they are not.
2) With an isolation transformer, your power source is ALWAY onboard, and your bonding is ALWAY onboard. In this case you can permanently bond in one single central location.This is much simpler, much easier to get right, and conversely much harder to screw up. Bonding is typically done at the main power panel.