Are you using dry chemicals to develop the film? If so, maybe they're not fully dissolved.
I use the MDO54 and the twirl stick with no issues. But I also invert the tank twice during developing.
If nothing else, shoot a sheet, develop it, run some stop bath (not water!) on it and check it before you fix it. If the blotchiness appears, then you know it's in the developer stage and not the fixer.
The reason you don't see it on the reveal of the film is that portion of the emulsion has been completely removed by the fixer. So any blotchiness will not bee seen there, but may be visible with the above method.
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