So I seem to be having some trouble figuring out how to use Vuescan's densitometer function; I have tried googling, but the only tip I could find-- pressing the cntl key-- doesn't seem to work. I've tried all sorts of keys, but all I get is an RGB number b/t 0 and 255.
When I adjusted exposure, this number would change, so I tried to control for that by including pure white (the opaque negative holder) and pure black (empty space in negative holder) in the crop and locking the exposure. The opaque parts read as 255, and the empty parts read as 0. I have my brightness setting (corresponds to midpoint gamma, AFAIK) at 1, the default setting. I don't know if this is a good enough control, but here are my results. To get these value ranges, I took several readings at random points on the film pieces.
Cleared film leader of 135 size Tri-X: ~51-54
Unexposed but developed section of 120 size Tri-X: ~50-53
Unexposed but developed section of crappy 135 size Tri-X (two samples from two separate rolls): ~63-65, ~68-70
You'll notice that the cleared film leader had a slightly (perhaps insignificant) higher range of readings than the developed 120 Tri-X. My thoughts are that, if there is a real difference (especially as one would expect the base density+fog of the developed sample to push it higher than the base density alone of the cleared sample), this a result of the 120 size having a different film base than 135 (though you had mentioned you thought 120 had a higher base density... curious) and/or it has something to do with the purple tint that is pretty well removed in the developer step, which is obviously absent on the fixed-only cleared sample.
Are these numbers significant? In my searching I don't think I saw any methods of inputting these 0-255 numbers into the density equation transmission density=-log(2^(meas/reference)), so I'm really not sure how to interpret my results.
Regardless of all this work, the fact that 120 film does not suffer the same problems 35mm does is a huge help in narrowing down possible causes. I have since removed my 120 film from the place I normally store my film, just in case. I haven't gotten around to buying a new roll of 35mm Tri-X (hey, it's Sunday, gimme a break!), but I'll do that soon to control for my storage issues.
If it is a matter of storage, I assume it is my fault. Even after the other unidentified cause, which I highly suspect existed (as my development problems existed long before I started storing film the way I do now) but never really pinned down was eliminated, film purchased at different times and from different vendors has all shown the same behavior. [Sorry for that freakishly ugly sentence.]
It's not like I store my film in a particularly strange way; I keep it in boxes/canisters in a dark, relatively cool wooden cabinet. Perhaps some other item I have in there is putting out low levels of radiation. It is also possible that something was releasing aromatic compounds (varnish in the wood cabinet, etc.), but I have my doubts that such contaminants could work their way through 35mm containers so easily.
FYI, I have had similar symptoms on rolls that have been purchased from multiple different vendors and have never gone near that cabinet (different cities), hence why I am so suspicious that I had another source of error and that storage was not always the problem. I admit that it is very ugly science, but I didn't have the sense to write down all these variables at the time.