You said this rotated at 75RPM? That’s really, really slow.
Very hard for me to believe that any significant about of distortion could develop due to centrifugal force.
But, one thing that was never mentioned - were the bags printed?
I mean - was there a distinct edge that was supposed to line up with the opening of the bag?
Printed yes but no need for a pattern repeat.
Are you really sure it was the shaft? I sketched out the apparatus and it became clear to me that once you got 14 k of g in a fpd, the whole mechanism began to oscillate and produce the shorter bags.
Ths shaft was only a problem because my micro switch setting was set too sensitive. A slight push in on it and I dont think it would have done this.