I have a long Ethernet run (about 280 ft/85 m) that goes through a conduit between two buildings. On each end, I have an APC Ethernet surge protector that is grounded to the main ground for each building. While I had some trouble getting it to work at first, once I stumbled across Zyxel's very fine 24-port switches, it has worked really, really well.
Then, a storm hit and the link quit working. As far as I can tell the switches were fine and I've tried replacing both APC surge protectors. It appeared the cable in the conduit -- which has a water leak in it -- was damaged. However, I tried new, better insulated cable and it didn't work (either through the conduit or running on the ground). On the other hand, I had three spare 100ft (30m) pre-terminated cables that I coupled together and that worked just fine running across the ground. I can't imagine why three unshielded cables patched together would work while nicely terminated, shielded direct burial grade Cat5e cable would not.
There is one difference I just observed after putting everything away for the evening: I've been using the TIA 568A wire pattern to the RJ45 connectors and the pre-terminated cable used the TIA 568B pattern.
Could that make the difference in signal loss? Can you think of anything else that would cause 3 patched together cables to work but one solid run not to work?
The only practical difference between A and B in this case is termination order.
The only way to know for sure what the problem is would be to get a professional cable installer to come out with a cable certifier and test your cable.
However, for the cost of having someone come out and do that and implement whatever repairs or mitigations are needed you could easily buy fiber and transceivers or media converters. Do that instead and save yourself a bunch of hassle and money in the long term.
If a storm is involved, it's possible you got a ground potential difference between buildings sufficient to cause a fault in the cable. Is it possible to check continuity on all the conductors and shield?
This is the primary reason for running fiber. I pulled 150' of fiber through multiple 90 deg bends in a 1-1/4" conduit, along with one each CAT5e and RG6U-Q. No problems. Get pre-terminated fiber cables from Lanshack (quite satisfied with these guys). The LC/LC connectors will readily fit in 1" conduit.
However, if you were working satisfactorily with the CAT5E (direct burial), can you just pull another one? Use the existing cable as a pull rope, and pull a string along with the new cable. Don't forget the pulling lube.
TIA-568 A/B makes no difference. The signals know not the color of the insulation. There is no difference in the twists of the different pairs.
Water in the conduit won't affect direct-burial (gel filled for that reason). It may affect a wiring closet if either end of the conduit is down grade from the source of the water.
Electrically, there is no practical difference except termination order. So long as each cable run follows the same standard at each end it will work and perform the same.
However, if you don't follow either of those standards then yes, it'll either not work at all, or could be prone to a high error count.
Essentially the twists are for a signalling pair. If a +/- pair are on different twists in the cable you will likely get noise induced into the wires and cross talk problems. The 568A/B standards ensure that +/- matched pairs from the ethernet port are on the same twisted pair.
I hope that makes sense.
TIA 568 A uses Green/Blue.
TIA 568 B uses Orange/Blue.
Green is twisted with more rotations per meter than Orange is.
I have no idea if either is preferable.
The only speculation I can make is that if you are doing a number of long distance runs in the same cable path, it should theoretically be slightly better to alternate A/B/A/B/A/B, etc... to minimize inter-cable cross talk.
I have no research to back any of this up.