1) Library resources (cache, preferences, application support) are NOT shared between 3.7.X and 4.X. In the case of strange problems dumping these folders can help to get everything back to square one. 3.7.8 and 4.1 are completely independent.
2) Capture Integration experienced similar problems with a back's communication jamming up and requiring a system restart to get back and working, BUT we experienced these problems with 4.1 BETA. Note that the installation instructions for 4.1 clearly state you need to completely remove any previous versions of 4 before installing. This would be a good place to start.
3) I've now shot 5 backs on three computers using 4.1 and have had no problems with any of them. That said there are a lot of combinations of backs/bodies/computers/workflows. Phase One DOES test thoroughly, and is very dedicated to solving problems that customers have. If you are diligent with recording the circumstances of the problem (which I know can be hard if your in the middle of a shoot) and honestly follow the suggestions of your dealer and Phase One your problem WILL be fixed. 99% of the time there is something small (a setting, low batteries, bad firewire cables, non-recommended firewire cables etc), and 1% of the time the problem is more subtle. The 1% are the cases you hear about the most because of the frustration involved, but if you bought from a dealer with good support and you work with them, you will have your problems resolved.
4) P1 Support does NOT come through their forum. That forum is marked very clearly as a "user-to-user" forum and the P1 support staff only answer questions on there as they have time. If you have a problem and you need a fast response you need to start a support case with you and make sure your problem is resolved. Your dealer is more than happy to do this on your behalf, because happy customers are our best marketing, and personally is my greatest sense of job-satisfaction.
5)
http://www.captureintegration.com/2008/02/...sync-my-iphone/ this will explain how to prevent 4.1 from launching when you plug into your iphone. thanks for this one go to chris
5) 4.1.1 was a very minor release that basically compressed the installer for faster downloads and made one very minor fix. Still if you do go through my suggestion to clear off previous versions of 4.X and reinstall then you might as well use 4.1.1