Leave the film in the fixer for twice or thrice the time it takes for it to clear; that will make sure any remaining silver salts are fixed out. Once the clearing time doubles from its original value, dump the old fixer and make some fresh. Exhausted fixer may never completely remove undeveloped silver salts from the film. Remember, T-Grain-style films like Kodak's T-Max range and Ilford's Delta range take twice as long to clear as conventional films, so you double the fixing time for those films.
The other way to ensure proper fixation is to use the two-bath method as you would with prints. The first bath removes most of the silver and the second fresher fixer completes the job. When the first fixer is exhausted, chuck it out and replace it with the second fixer, which you then replace with a fresh batch. Repeat this cycle x5 then start again with two fresh batches of fixer.
You're paying the price for taking shortcuts. C'est la vie.