OK. I managed to get client and (non-bukkit) server updated. I can't test non-bukkit server (I run a bukkit one) so I'm doing the bukkit thing at the minute (which is taking a long time- man that's annoying).
Zippinous, I can supply you with the diffs that make this all work easily enough so you can patch yourself back up to date.
1. As in temp fix 1.
2. Allow indirect redstone power to the machines. (as suggested by me previously a long time ago)
3. TileEntityRotary, TileEntitySingularity, TileEntityCenterfuge all have their recipe methods changed to copy their recipe list from their original versions.
4. mod_IC2_AdvancedMachine implements IOreHandler and in the handleOre method refreshes the TileEntity recipe lists. This way, anything added to the originals will automatically get added to the advanced versions.
Tested and verified with RedPower ores and with BioDiamonds IC2 mod to work for both.
PS. Bukkit will follow tonight- but need to go do a day's work first.
Edit: Someone else can bukkit port if they want, and I don't mind it being linked on mcportcentral but I do request no adfly links please.