As of the most recent beta I'm having two problems: 1) It's impossible to edit the VM configuration, since the moment the VM stops Parallels quits. I have not found a way to keep it from quitting when it's not running a VM. So, I can't edit my VM configuration. 2) Parallels doesn't recognize the VM directory that I point it to. I only have a Boot Camp setup, but I have to double-click on the .pvs file in order for it to open. Even though I have the correct directory set in Parallels Preferences, every time I open Parallels it asks me to create a new VM. It doesn't remember that the Boot Camp VM exists. Trashing the .plist doesn't fix this.
The VMs you have are remembered in ~/.Parallels_Settings. Edit that text file to see what's going on. The autostart and autoquit settings are remembered in your pvs file on a VM by VM basis. Those are text files too and can be edited with a text editor. (Obligatory disclaimer: You can break those files by editing them. Be careful.)
In my .pvs file the variable AutoShutdown = 0 I take it this is the one that quits Parallels on shutdown? If that's the case, then Parallels isn't reading the .pvs file correctly (or something).