Make sure you are setup as the administrator when using Vista. This is the most common source of Vista issues.
For your truck, disconnect the battery for 10 minutes and then try and start it up again.
Please make sure you are running either the latest public release software 7.5.3
http://www.efilive.com/download.aspx, or if you are running BETA software please ensure you upgraded to the June 12th Release.
If you have upgraded software recently also make sure when you installed everything that you upgraded your firmware too (if you are using V2).
Then I'd switch everything off, and reconnect again. Start up PC, connect FlashScan (ensure you hear/see your PC accept the hardware - usually it's a dinging noise), then connect to your truck.
Cheers
Cindy