I'm loading my savefile and this mod just forgets about the waypoints already placed. All the old waypoints are visible and permanent but spidertron doesn't follw them. If I place new ones it's like the old ones don't exist, they stay as they are and don't change numbers or anything. If I clear waypoints only the new ones (placed after loading the save) disappear.

Savefile and additional required mod here:

https://www13.zippyshare.com/v/5CNRqAiB/file.html
https://www13.zippyshare.com/v/Rzfdasit/file.html

I'm very sorry about that. You'll be glad to hear that they are not actually permanent, they will disappear after 463 hours... :)
In the meantime, I'll fix it for 1.2 and clear all the previous ones as well. If you really need to, you could go back to your previous save file (and if you want to upgrade to 1.1, remove line 148 after reinstalling 1.1: https://github.com/tburrows13/SpidertronWaypoints/blob/v1.1.0/control.lua#L148). Or just make sure that there are no active waypoints before upgrading.

It's just a testing save so it doesn't matter in this case for me. But it would annoy me forever (=463h) if it happened to a savefile I cared about...

Yep fair enough. I can fix it for all saves in the next update, so no one will have to wait 463 hours :)