Parallels v6 w Win Vista Issues

I have Parallels 6 installed on my MacBook. I have been using it with no problems for a couple months to run some Windows based software until last week when I had an issue with some kind of SCSI(guessing name?) disk or configuration was missing.

I did some research and it said insert the Windows disk and fix the installation. I inserted the disk, set the bootup options to CD/DVD first and it launched the installation. Never gave me the option of fixing the corrupt previous installation.

So I just went ahead and installed it.

Now the problem is that I can load windows and use it inside of a screen. But it will not connect to or locate any of my existing windows applications that I was running. Although when I double click the applications it loads as if it is loading them in Parallels (starts up parallels and windows) but will never load the software I am trying to execute.

It will also not start or change into Coherence mode. Will only run as a seperate window now. Ran in Coherence prior to this issue flawlessly.