Transparency holes when exported into PDF

Hey guys,
I have a strange issue with pdf transparency that I just cant wrap my head around, probably because im not really a print guy, but anyway here goes.

Im trying to print some playing cards I have put together, the way I do it is that I have each individual card as separeate indesign file and then I link all these into another indesign file to put them on a grid (SRA3 size).

Issue Im facing is with transparency - I have some layers in the cards themselves (see image no 1) that need transparency. It looks alright in the card indd. It looks alright when I export the card indd into card pdf. It looks alright when I link either the card indd or card pdf into the A3 grid indd.

But then when I export the a3 grid indd as a final print pdf everytime I have these layers with transparency in those linked cards it makes holes into uderlying graphics (image 2) - uness I use X1a-2001 preset. And if i do that, I get issues with text quality when the page gets printed (theres some small 7.5pt text that just looks awful when printed with that old standard). When I use any more recent standard the text looks good when printed but I get these holes. The only thing that doesnt make holes are vectors but I cant use them for everything obviously.

I dont understand how is this happening and before I bake everything that cant be vector into one PSD I was wonderring if theres is something else that can be done.

Thanks for any pointers.