Boards can sometimes have an issue with plate through holes. If you've found one with a problem. likely all the boards in that batch will have issues - just not necessarily in the same location. Where the through hole devices are, I'd make sure the solder wicked through completely, and maybe even put a bit extra solder top and bottom to guarantee the connection. It also wouldn't hurt to solder a bit of wire in the vias and cut it off flush when done. That should address your marginal connection situation. Sometimes a track will "buzz out" fine, but contain enough resistance to make signals flaky if you've got a poorly manufactured board.
Your pull up resistors likely need to be smaller, not larger. The trade off is that smaller resistors consume a bit more energy, but speed up the rise time of the waveform. I'd try 2K2 or 3K3. I don't think I've ever used anything over 3K9, especially with multiple devices sharing the bus. 10K is at the extreme upper limit of the spec. Unless battery life is a critical design requirement, go small. 1K is the absolute minimum, so don't go quite that far.
Any chance you can share a picture of the board layout?
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