Whenever I open Wrye Bash it starts to flash uncontrollably and the Mark Mergable window comes up and starts flashing on and off.

It actually does it ANY time it automatically does its Mark Mergable. EXCEPT when I choose to rebuild my Bashed Patch. The only way I've been able to get around it is to copy a new Bashed Patch 0 esp everytime I need to rebuild it. I haven't switched to cbash at all. Should I try reinstalling it as a standalone?

Close. i got it fixed with the new SVN 1399