The rectangular cut on each string groove is what makes the bass strings go out of tune.
If you look at the empty bass string slots you can see the marks left by the strings as not reaching the bottom of the slots.
Use a needle file to shape the trailing edge curving downward those slots that bind.
Get a rounded toothpick wrapped with fine sandpaper and smooth out the slot(s).
Tune up, try it and repeat until they no longer bind.

I use a welding tip cleaner set for the final cuts on nut slots. The average set comes with a variety of sizes that will suit all string gauges. Great for that final smoothing over.

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