Reported to me by players on my server, using Apotheosis-1.19.2-6.3.1. This problem wasn't in previous versions, according to them.

That's uh, weird. The random that generates them is seeded based on the tower's position

There's multiple Item Frames per tower, each has the same gem inside. 4 per tower

seed: -2439561773624327919
/tp @s 432 ~ 880
generated 2 worlds with same seed but one with 6.3.0 version and other with 6.3.1
the one with 6.3.0 (prev version) has diffirent gems and the 6.3.1 (new version) has identical gems

to quote the player

Sorry, let me clarify. Gems are identical within towers. They're different per tower, but each tower only has the same gem 4 times.

Yeah same for me, different per tower, but each tower always contains 4 identical gems.