Helpful Resources for Version Cue
These updates are supposed to fix critical issues with both components. And yes, I'm pretty sure you can't run both servers at the same time. You should also try migrating your CS3 projects over to your Version Cue CS4 server. Adobe has a help article on this: http://help.adobe.com/en_US/Bridge/3.0/WSEAAF9554-6F4B-430b-92C0-AC60A7AE51BC.html
It's a little tricky but once you get this going, you should be able to run VersionCue CS4 and see you old projects in there. Also, check out this article: http://kb.adobe.com/selfservice/viewContent.do?externalId=kb407015&sliceId=2
Lastly, if none of those suggestions seem to work, I would point you over to the Version Cue Community Support page for more answers: http://www.adobe.com/support/versioncue/
