Dude: There are a lot of things that can go wrong, so if I sound reductionistic, my apologies. I have no idea how Cube works, but I've been using my 305 with KCS (on Amiga) with no problems. A quirk of the 305, though, is that the MIDI output from each part corresponds with that Part's number - thus, if you play notes using Part 3, the MIDI output will be on channel 3. Since you don't say whether you have a MIDI patchbay or not, I'll assume you do... and I'd look for trouble there first (like maybe Cube is only looking for incoming MIDI on channel 1 and you're on Part 3, or maybe the patchbay is re-channelizing the output from the 305). Try taking the patchbay out of the loop. Also, check to see if Cube will synch with the 305's internal clock - it might yield a clue.
This may be beyond my expertise based on the sequencing program, but my 305 has been bulletproof since I incorporated it into my rig. Let me know, and detail what you know the problem *isn't*, and I'll look for more failure modes.