Welcome to the world of MIDI code.
Although I do not use Cubase, I have faced similar problems, and the advice that I see here is good.
Let me try to explain it to you in laymans terms.
In Cubase, when you want the sequencer to initiate your 305 to a specific performance or set of voices, you have to go to the patch map and say Wired Lead track 1, Fat Bass, track 2, Analog kit track 10. By doing this, you are sending the proper PC (program change) to init your synth.
My guess is, when you want to add filter sweeps and loop your synth. You have set up your patches and you record your eight measure. The problem is you have not told it where the start point is. So if you got your first 8 measures to play properly, you probably MANUALLY set your synth at the beginning of the sequence.
No problem.
Every sequencer worth its salt will let you access the MIDI code. The question is how. If you don't want to read the manual, help will tell you how to access it.
I hope this put into perspective all the other advice that you have received.