When you fix negatives, with rapid fixer it shouldn't take more than about 30-40 seconds to clear a film strip. Upwards a minute and it's time to replace it. Just take a piece of 35mm film, like the leader you trim off before you load your film into the reels and tank, and dunk it in your fixer with agitation.
Even though it takes no more than about 30 seconds (or less) with fresh fixer to clear a film strip, it isn't a bad idea to fix for five minutes using Ilford Delta, Kodak TMax, or Fuji Neopan Acros. If you use traditional grain films, you can probably get away with three minutes, although five minutes will not hurt a thing.
Good luck, and I hope the re-fix solves your issues.