Stabilise, paint and precomp question...plus freeze frame..

I have a close up tracking scene ( across three wine bottle labels)... that required  stabilising.
It also required some paint on some 100+ frames to remove a small hair that had floated in.
Easy stuff but...
When it comes to retouching (paint clone) on the stabilised layer...it was not stabilised and the cloning was thrown by the "Analysis"!
So I tried a precomp (New Comp) to paint on..  This also ignored the stabilise FX even though it was in the new comp. You dont find out until you finish painting!!!!
I reverted to exporting a DI and painting on that. Worked as one would expect it to but it is a generation and extra effort.
Anyone know why the precomp did not stabilise so I know for the future?
I next wanted a freeze frame at the end of the DI track to hold it longer.
Duplicated the layer and froze the frame.
This created an issue with the paint on in both layers where I could see the paint and it was shifted off position!!!  weird!
I reverted to exporting a Frame and using that instead.
Any thoughts or known issues with stabilising /paint / clone that might cause that?

When you precomped, did you move all attributes into the precomp?
What (exact) version of AE are you using (down to the last decimal)?

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