The 3rd one had an interesting difference - it allowed more sound/signal to pass through most of the time, but I noticed a delay; I'd pick a string, and there would be perhaps a 1 second delay before the sound was produced . . . but once I started picking/strumming, the sound was flowing OK (unless I just didn't notice the delay continuing to occur). I tried a regular 6' CAT 5 network cable, and that worked fine. I then bought a Belkin 25' CAT 6 network cable (if anything, CAT 6 should work better than CAT 5, as far as I know), but that didn't work - that caused the intermittent sound again. I'm of the opinion that the length is the critical factor, based on my own experience. However, I nevertheless see posts like yours which reflect people using a 25' cable length, apparently without any problem. Any thoughts as to why the Line 6 25' cable hasn't been working for me? [One other thing, to confuse matters . . . I noticed each of the Line 6 25' cables I tested worked OK when connecting my Variax guitar to my older Line 6 PODxt Live. I can't figure out why the cables would have worked with the PODxt Live, and not the POD HD500X.]
I've been using the longer cable since day 1 without any issues like those you have described. For the lengths we're taking about, there really shouldn't be any difference at all, as the signal leaving the guitar through the VDI is entirely digital...it's all 1's and 0's. The signal will either reach the POD or it won't. Signal degradation shouldn't come into play much, if at all, between a 6' vs 25' cable, as it might with analog.
Crackling, or intermittent sound must have some other cause...either the jack on the guitar or the POD could be the culprit.
The latency is another question. If you're actually hearing 1 full second of latency, that is an absolute ETERNITY, and would be impossible to work with. Much above 20 ms, latency becomes very noticeable, and will handicap most players.
The good news (sort of, lol) is, it sounds like you've done all the troubleshooting you need to do. The fact that both the guitar and various cables work fine into a different amp, strongly suggests that whatever the problem is, lies with the 500X. You've already ruled out everything else.