OK, To be clear here.
You have multiple Xerox devices and one FujiXerox that all have the same problem even though the FX and Alta have no common traits, are made entirely independent of each other and run firmwares developed in different parts of the world.
And it can happen even when eFax plays no part, so a scan to SMB/EMail/FTP/USB will all show the same issue making eFax not a worthwhile thing to troubleshoot.
And the Lexmark works fine with the same job via eFax.
That should make it real easy to test then, reply with a pdf I can print that will have the problem when scanned, as well as a scanned Configuration report from one of the AltaLinks and I will do a scan to see the issue for myself and troubleshoot the problem in-house at the Xerox lab.