I’ll be mostly saying what’s already been said, but I’m posting it on the off-chance that it’ll help you. Issues like these are frustrating and very time consuming, so any hint as to the cause can be a great help.
Are you sure you are not using welds for any animation? Despite however sure you might be, you might want to check using game.ItemChanged (or use one I wrote here).
I once debugged an issue like this where one single Weld updating on every render step limited cluster updates and caused parts to not disappear or reappear as often as they should. One thing to note is that this seems to happen more easily with Unions. I have no idea if that extends to MeshParts, Parts with meshes in them, or why it affected Unions more. The performance of cluster updates was not the same among multiple computers: some updated slowly for one reason, some updated slowly for a separate reason.
Here are some posts about cluster updates you can read through. Maybe they’ll help. Here is a post where I talked about my experience with this previously.
Also good to know: Shift + F6 turns on the profiler, which might help you find out the cause of the problem.