Please try version 1.14 from github just to make sure your bug is not already fixed.
Just to make 100% sure, please check that your "universe bios screen" looks like this (but with version 3.2 not 3.3):
Not some gray rectangle "warning" window asking you to press a key, right? If you get a "warning" window and not the above universe bios screen then your Universe bios is not working correctly in PFBA.
Otherwise, if you still get flickering even with the latest version, we have to find a way how I can reproduce the problem on my system because I don't see the flickering you mentioned. Once I can reproduce it I can fix it hopefully.
Is there an example rom that loads pretty fast where you see the flickering? Is there still flickering if you use some other bios, different than unibios?