I had a very similar situation in a relative's office - a certain system kept dropping packets and we swapped everything to no avail.
Turns out it was because of RF interference, or that's what I thought the problem was. I swapped a dozen different cat5e/6 cables and the only one that worked was a shielded one leftover from some in-wall installations in the building.
May or may not be the case with you, but it might be worth a try.
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