Ok I've always had problems with games not filling up the entire screen. Instead I get black borders. I solved the issue with a few games by upgrading 1.53 from 1.43 and by unchecking enforce aspect ratio and extend snes height.
However with a few games like Knights of the Round the border problems are still there no matter what I do.
I have the same problem in almost every emu, luckily for you I had the solution for almost every emu. You need to know how to compile the source yourself though...
Assuming you can compile it (look elsewhere for a guide and the libraries required), you need to modify the blitarea.top and blitarea.bottom values in winlink.cpp. I am at work right now so I dont have the source to tell you how exactly but dont worry I will update this post with the info. Btw one the worst offenders is Final Fight 2