Sometimes I have situation like that. For example for Koeln this situation occurs only for one alternate kits, for bayer leverkusen for all three alternate kits, for fc barcelona, real madrid, arsenal none issue. I have just moved fifa16 FIP5.2 kits from season 2021/22 to fifa15 chaos patch but I didn't replaced home,away kits just added those new kits as third ones, so for most of teams we have now 4-7 kits for example bayer leverkusen:
But this problem occurs and I don't know why. When I unpack rx3 files kits are OK, in FIFA16 FIP 5.2 they are visible in game. Maybe there is too much kits now in teamkits.txt database and game engine cannot handle that. Nevertheless I will leave as it is, so user just will not choose such kits, but it would be good to fix that if possible but I don't know how.