I just happened to look at the Task Manager today and found that I had five instances of RedGate.SQLCompare.UI.exe running, though I had no visual instances running. I likely ran SQL Compare five times yesterday and though I closed it each time, it appears that some thread is still alive despite having closed the application.
I'm running Windows 7 64-Bit, SQL Compare 10.1.0.102 Professional Edition, SQL Server 2005/2008, Source Gear Vault 5.1.
Considering I've had other issues with SQL Compare complaining about being unable to delete files, I wonder if this is related. (I'm thinking that the instances that will not close out are holding onto files.)