I've got some Lava Crystals in IC2 Generators, and they were working fine. However, when I remove them and try to put them back, they ceased to work in the Generators again.

It's probably something on IC2's side.
And you got off easy. I tried the same thing with one of Extra Utilitie's generators, and it set my LP network to something like -1000000.

Well, they do update something like 5 times a day.
Was bound to happen eventually.

Yeah, IC2's side. It did work for over a year, so they messed up their s*%@. Fun fun!