I spent the evening experimenting and came to the conclusion that the reason is the one expressed by @Slak_Jaw in the first reply.
My songs are all on Apple Music Sharing but probably from the iPad it doesn’t get exactly the same version as the Mac and messes up the hot cues. I solved the problem for most of the songs by re-inserting accurately the same version on both the Mac and the iPad, for some (very few now) it doesn’t get it, but for the majority I solved it.
Thank you all!!!
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You’re welcome @Bassbara. Thanks for the follow up.