Sterioma, sorry for late answer, I don't have internet connection at home...
To be honnest I didn't try to use 50mm lens for 6x6 negative. Me too posted simillar question to use 80mm lens for 6x7 negative (normal shoud be 90mm). I was told in my case there is no problems. I belive you will rather have probelms with distorsion not with vignetting with 50mm lens for 6x6 negative. But, again, I didn't try so this is my thinking, not fact.
I belive your problem in first place is caused by wrong condenser. Try to get condenser for 6x6 negative. And use 80mm lens. As I told before, those thing in these days are so cheap, I belive you should not have problems to buy them.
Using 50mm for 6x6 mask I think can "capture" mask but not vignetting image. But, as I said I didn't ever used 50mm for 6x6 so this is just my thinking, not fact.
Again, with todays prices you should really get propriate dondenser and 80mm lens. If Rodenstocks, Schneiders are too expencive, try Meopta Anarets. While 50mm Anaret I had was not good lens, 80mm Anaret I had is good lens. And it is cheaper, new or secondhand, than Rodagon or Componon-s. I think for 100 or 150 USD (or even less)that both condenser and lens would cost, you really should buy them and avoid probelms you have now. Atleast that is what I did. I bought condensers, mixing chambers and lenses for all negative sizes I use.
Saying above: Meoptas Opemus 5 I used before had only one condenser and only one mixing chamber. It has not option for changing condenser or mixing chamber. U used it for 35mm negative and for 6x6. But, I used 50mm, lens for 35mm negative and used 80mm lens for 6x6. I had problems with 50mm lens (light falls on one side of print), but when I replaced that lens for Rodenstock 50mm lens my problem was gone. Never had problems with 80mm lens.
So, try to get 80mm lens and condenser for 6x6. I think this is best you can do for beginning.
And do contact
www.meopta.cz. Every issue I had with Meopta enlargers and theire products I had, even if my equipment is long time out of production, I was able to solve contacted Meopta.