Big +1 for GPX Magic. One click fix does a remarkably good job. For better refinement, explore the different tabs. For example, I find one-click can generate corners a bit more rounded than I sometimes want, and the profile can be a bit too smooth… but by customizing settings, it’s excellent.
There’s also processGPX on github, which is a command-line tool I wrote in Perl. If you like that sort of thing, let me know here. But over time GPXMagic has adopted a lot of the functionality I put in that code, so you don’t lose anything with GPXMagic.
If you post the GPX files here, I can try to improve them for you (with a combination of those two tools).
Just taken a quick look at the Magic Road report… it’s not going to be as simple as a “One-Click Quick Fix” after all. There’s an out and back section (I’m guessing that’s where the glitching occurs?), so it’ll require using the GPXmagic “Route maker” tool if you were wanting to sort it properly (that tool was designed specifically for this scenario).
Why it happens… In Magic Roads the road is generated about 1.5km in front and behind the current rider position. When you get to an out and back section it’s generating both the out and back roads at the same time. If the gpx trackpoints aren’t in exactly the same position in both directions, you get all kinds of weird and wonderful rendering (signs in the middle of the road, riders sinking into the road etc. ). The “Route maker” tool sorts all this out. I’ve used it to sort a few out and back routes and they work perfectly now.
If you’re not bothered about getting to grips with GPXmagic, then as @Dan_Connelly said, post a link to the gpx file on here and one of us will be able to sort it out for you.