Ok, I did a factory reset on BIAB and on the Focusrite, and believe it or not, it all worked. I hate to get beaten by Windows and the sound issues.....

Resetting/reinstalling the audio interface driver and settings definitely made a difference although I am not sure why. A RTFS of BIAB helped as well.

Again, I only recorded a couple of bars of guitar and the playback seemed to line up ok with the backing track. I wouldn't use it for any serious recording, for this I export the backing track and use it in Reaper, or use Realband occasionally.

Now that it works I am happy to try our a few things for anybody experiencing issues.