I think I've figured out what might be happening. I have a small Cakewalk project file that reproduces problem. The first track was manually entered, the second two were imported. The manually entered midi data is fine, but the imported tracks appear to have a midi event embedded which causes Z3TA to switch to arp patch 1 (the first patch) from CC/Hard Lead/Fat seq. As far as I can tell the event isn't recognized so it doesn't show up in Sonar, I used another midi editor to find it and get rid of it. Removing the offending midi event fixed the problem once the midi was re-imported. Is there a way to get Sonar to show all midi data regardless of whether or not it knows what it is?

Is there a way to get Sonar to show all midi data regardless of whether or not it knows what it is?

Views -> Event List [ALT+8 shortcut].  From there, you can highlight an event line and hit the DELETE key.  Unless something really funky is going on with Sysex messages, you'll be looking for Program Change ["Patch"] commands.

 Nope, like I said it didn't show up in the event list or the sysex list. The other midi editor I used showed it as an unknown event.