Some problems in the Alpha 6 version (not sure if they were present before since Alpha 6 is the first version I've tried):
1. Any type of reactor plating does not work as intended in your reactors. It does add the extra heat capacity, but it keeps adding it again every second. This is evident with a panel from nuclear control, which shows the values for max heat and meltdown constantly increasing. Similarly, when removing the plating the extra heat capacity is not reduced back to normal values. To ensure that the problem was not with the info panel, I tested the reactor itself by removing all heat plating and letting it heat up with a few plutonium quad packs. It was able to far exceed the normal heat maximums without it exploding. When exiting and reloading the world, the max heat and meltdown values return to normal: the test reactor exploded immediately on world load.
2. Another bug regarding temperature. If a reactor heats up past 32767 heat, it loops back around to -32768. Are you using a short to store heat values for your reactor? This causes effects such as high-temperature breeders not being able to reach their intended operating temperture, and the ability to safely run a high power reactor with no cooling whatsoever.
3. Not quite a bug, but perhaps an unintended behavior due to the way Greg changed Thorium. From what I can tell, ender chambers only vent heat when the reactor produced heat during the previous reactor tick. Thorium cells, however, only produce heat every 5th tick (or 2/5 and 4/5 for dual and quad thorium cells). This results in the ender chamber effectively venting significantly less heat for thorium-only reactors, as low as 6.4 average heat per reactor tick if only single cells are used. This would be easiest to fix by simply letting ender chambers vent their heat every second regardless of whether heat was produced the preceding second. This would also make ender chambers more effective for MK. V reactors (where they're also less effective than normal due to being off for some portion of the time). Personally I don't see why they wouldn't simply vent heat every second, regardless of whether the reactor is producing heat or is even on, but maybe there's a design consideration you have that I'm not thinking about.
Edit: I should probably add that I definitely tested issue 1 with normal IC2 reactors, and I think I tested issue 2 as well, and did not have either problem with the classic reactor.