I upgraded from Vista Home Premium 64 bit to Win 7 Home Premium 64 bit and I didn't get any notice to uninstall WindowBlinds. One thing I did though do was reset the skin back to default. I have Object Desktop so I in fact reset everything that change things like icons, cursor and what have you back to default before running the Win 7 update.
Don't know if this little bit of information will help. 
EDIT: Just noticed you are talking about WB 6, I had WB 7 installed, sorry. If you reset the skin back to default before uninstalling you might want to try a clean up program like CCleaner, and use the Registry clean up function.