bvy,
First, your fixer is likely working just fine; fully-fixed film has a lot of other stuff in it, most of which is supposed to be there, that keeps the film from being completely clear.
Fixing way too long (e.g., overnight) could:
1. Bleach out the base fog on the film. Every developed film has some base fog. It is a normal result. This makes the clear portions of film a bit denser than the clear plastic base would be, but that's how the system works; it's supposed to be there. If you had fixed a negative with an image that long, the image would be bleached as well.
2. Remove other components in the emulsion. There are some sensitizing dyes, etc. that often are still in the emulsion in residual amounts even after proper processing. While not altogether desirable, these are also accepted in fully-processed film because more fixing or other treatments needed to remove the dyes would adversely affect the image. So, they are kind of supposed to be there too.
3. Remove the emulsion entirely. The gelatin emulsion on the film itself can be removed through extended wet time. The gelatin swells and separates from the film base. If this happens, then the remaining acetate film base is very, very transparent in comparison to the film with the emulsion on it. The emulsion is definitely supposed to be there
Any of the above could explain what you are seeing. However, whatever the reason, it is not underfixing that causes this. Don't blame the fixer or the time-tested and accepted tests for proper fixing time.
If, however, you suspect that your fixer may not be doing the job, test it against freshly-mixed unused fixer to see if it clears as well as the new fixer.
Best,
Doremus