Julia, you might want to post more details about your fixer -- what brand and type is it, how did you mix it, and how long are you fixing? Proper use of fixer varies from one brand and type to another. Most notably, fixers based on ammonium thiosulfate ("rapid" fixers) typically fix paper in a minute or so, whereas fixers based on sodium thiosulfate (conventional fixers) take substantially longer. If you're using a sodium thiosulfate fixer with times appropriate for rapid fixers, this could explain your problems. Likewise if you've over-diluted the fixer because of a measurement error or mis-reading the instructions.
Another point: Bad fixers often acquire a rotten egg odor and/or a precipitate. If you see stuff floating in the fixer bottle when you stir it or if you smell rotten eggs, you should discard the fixer.