Okay, I've been chatting with Algorithm over on AE's MCF thread and he believes that the stacking bug is completely on IC2's side. The relevant part of his post:
QuoteI don't see why forge would be involved the inventory has a stack size, and in the reactors case it returns 64, the item also has a stack size ( 64 ) I would think that making the inventory have a stack limit of 1 would solve the issue, plus you can easily get the shift clicking behavior to fall in line, I do so with the wireless access points, as the WAP's them selves have a different stacking limit then the normal 64 items per stack for boosters.
The Forge mention is from the fact that I brought up the fact that someone made a note on the bug report I submitted on the IC2 bugtracker saying that they believe that one of the IC2 devs mentioned that this whole issue was a bug inside Forge as well. I'll make sure to make a note on my bug report linking to this post.
I wouldn't say this is a game-breaking bug, but it's a definite annoyance.