Well, first of all congrats for getting a 100kVA generator off the ground and into the sky. As I figure it, 100KVA operating at nominal aviation DC 28 volts is capable of producing 3571.43 amps. That is one big-azz generator.
Next, the answer to your question is a complex case of the dielectric breakdown voltage as it relates to pressure altitude. There is an elec coronal inception, or streamer formation on some part of the generator which finally arcs and trips the breaker as you increase altitude where the breakdown voltage becomes lower.
If the aircraft has pressurized generators, I would investigate the pressure system for leaks, or tears in a bladder or hose. Or possibly it is not pressurized, in which case I would investigate the generator internals for gaps which are lower than the specified tolerance for the service altitude that they are rated.
The general rule of thumb is that the air gap between conductive fields @ STP to prevent breakdown is about 3 million volts/meter(I'm doing this from memory, so go easy on the math). This is increased by about 1.5% for each 2500' elevation up to 30,000' and about .8% increase in dielectric distance for altitudes above 30,000 each 2500'. There is of course, inter dependencies on the shape, size, and purity of the conductors, but I think we can ignore that as the problem likely is in the stator area where the field is charged, assuming it is an alternator and not actually a generator. If a generator, we would look at the brushes and the commutator.