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Notes -
I think the specific issue is that the DTFs are stiff, hexagonal core strings. It makes it hard to get the intonation right. I'm wondering if the round core flats would help with that, since they tend to be more flexible.
I doubt it has anything to do with "flexibility" unless the strings get physically caught in the bridge / nut slots (in which case the slots may need repair work). Bass strings just don't work all that well if the tension is too low. Have you tried recording a single note and checking the spectrum?
Here is what quick googling returned as one possible cause for issues that might be perceived as intonation problems: https://link.springer.com/article/10.1007/s42452-020-2391-2 (string inharmonicity).
See if you can buy a regular cheaper non-hex core bass string and try if that also suffers from intonation issues. That is at least a cheap test and being flatwound vs roundwound should make no difference to that (at least I can’t come up with any physical basis for one).
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