If you have a cable that's long enough, or can buy a good one for a price you like, I'd suggest running it as a test outside the walls to both ends, to see if it negotiates and stays at gigabit. This works best as a test if you can leave it for a day or so, which is often awkward or unfeasible. If you still get negotiation issues, then it's probably a port issue. If it works, then reterminating the in-wall cabling is normally the next step.
That takes tools that you probably won't already have, and knowledge you probably won't have, either. You can buy the tools and probably find instructions on Youtube, but the investment in doing that for the first time is substantial. It is, however, super easy afterward, and a good skill to have. It's so easy that most folks who've done it already will routinely recommend it as a solution, forgetting how intimidating it is the first time.
If THAT doesn't work, but an external cable does work, then you're probably going to have to re-run the wire with something new. That's a giant PITA, and you usually have to buy a spool of wire, which is a lot more expensive than it used to be. (massive boxes of Cat 5e wire used to be cheap.) But you should at least have your termination tools already, so that part will be easy.
But, damn, running in-wall wires sucks.
If you feel well-heeled or don't want to deal with any of that, remember you can hire pros for troubleshooting and wire replacement. This will be very expensive in comparison, but the amount of hassle avoided can be well worth it. Getting all sweaty from hot crawlspaces, and then itching for days afterward from all the fiberglass, is a whole lot of No Fun. Remember your mask discipline, you don't want fiberglass in your lungs.
edit: if you do end up having a pro run your cable(s), consider running fiber as well. You'd probably want single-mode fiber: it's more advanced, and requires better optics to drive, but the price difference on the optics isn't large anymore. (it used to be gigantic.) You can get wall plates with both fiber and ethernet jacks, so you can just light up the fiber, someday when you're ready, by plugging in the right cables. (use LC terminations, they're kind of the default.) The cost delta should be relatively small.... the really expensive part is the bodies doing the pull. The cost of the fiber and the extra terminations should add only modestly to the price.