I know at least 2 of these are known bugs. However unlike most of the posts i've seen on here about them, I've found ID Conflicts (server only strangely enough) for 6 blocks in IC2. All of these blocks function normally under SSP but have a Block ID Conflict on the server with the exact same settings between server and client, with the exact same versions of mods installed appropriate to client/server. This is under Minecraft 1.2.3/Server 1.2.3. The blocks are as follows:
To get a log file of this info, run your server through a batch file. at the end of the line that runs your minecraft server put >>log.txt and it will output everything up until when mods start loading into a text file, and then any commands entered when the server is up.
I edited out my user name (obviously) and left out none conflicting block ids. Finally, again, these only conflict for the server, and I believe this is either the cause of the problems, or are closely related since everything works fine on SSP with the exact same config files.
EDIT: Note: I've been encountering invisible nukes, nukes crafted swapping into luminators, etc. for at least since 1.8.1, dunno if its been happening longer than that or not though.