Did you follow the instructions listed here under "How To Pictures" tab at the link you provided for the AM Shifter at Andy Mark? Aligning the disk clips at the very end of the back of the hex output shaft. Means you would not use the alignment tool usually provided w/ the encoder I would think.
Or are there spring clips missing from the hex end of the output shaft on the other side allowing the output shaft to back out the other side? (The ewncoder side). We usually cut the shafts for clips on the wheel side ourselves.
http://www.andymark.com/product-p/am-0957.htm Click on the tab below it marked "How To Pictures."
Good Luck!
(After a much closer review of both the Docs and the How To Pics there at the Andy Mark Link above....Something is definitely wrong...The Docs and the pics do not even match...I'd contact Andy Mark ASAP). The installation shows 180 degrees different in exactly how those should even be mounted according to the Docs and How To Pics.
Looking again, the completed pic at that link showing the whole (am-0957) for sale...NOTE: Use the magnifier on the pic...It shows no encoder enclosure cover on that completed encoder...Just the wheel clips lined up w/ the end of that shaft. So, maybe you cannot put the normal encoder cover on w/ those particular shifter gearboxes. (they do work without the cover...That I do know. If a cover is snapped on and that shaft floats outward, it would break that mount. I'm sure if a cover was supposed to be attached, that completed gearbox pic would show it attached. Did you have a cover attached to the encoder that broke the mounts? The How To Pics don't show a cover either...But I wouldn't think they would given that all they are trying to show there is the alignment of the encoder wheel clips to shaft end.