They do not appear to be saving in single player for me.

Can you please do the following for me:

Can you take the files from:
%appdata%\SpaceEngineers\Storage\363037395.sbm_WaypointsMod

And post them to pastebin.com (should be one .log files and a .txt file with a very long name). And then paste the links here? That would help me track the problem down.

I am also having this issue and cannot locate either of these within the mod to send. perhaps this is the problem. 8D

First file name = c6e1b1e5-035f-4acb-93f1-3e2db07f9c53-Settings
First file contains no text
Second file name = Waypoints
Second File Text = [09:27:38] Script Initialized: v0.1.0.2
[09:27:39] Clearing
[09:27:39] Count: 0

reffnerc, those are indeed the files I need. But can you do me a favour. Run the game, add a few waypoints. And then upload the text of those two files. And after you do that, run the game again and then show me the files again. That way I have an idea of what is occuring.

I have that issue sometimes, too, though I'ld say it saves over 90% of the waypoints. Couldn't it be an issue of the savegame in my case? Normally all my wps appear, only once in a while ONE is missing.
I'm trying to make up a "bus stop" system - cargos showing up at wps waiting to be loaded and than go on - which worked before the last patch. Now Autopilot has issues (in my game) and the whole thing crashes badly when a programmed wp is missing. ("Crashes" means cargos spinning around like crazy and remote control can't be stopped - reload of the game is the only remedy I found so far).

ether i found a bug, or the owner of the server im playing on managed to 100% disable all waypoints from being seen. i tryed /wp toggle and still cant see them. when i asked owner, he said he didnt do anything with the mod. search solsystem, i have no idea if anyone else is having the problem or its just me. i tryed relogging and nothing fixed =/. tryed adding a new one cant see that also. but /wp list does show that all the waypoints are there.

There was about an hour where the publish I did on a fix didn't publish properly, and it was missing an SBC file, making the waypoints not display. This should be fixed though.

ok, sounds good ill tell the owner n see if he restarts the server and hopefully the server will update the file.

Good to know, my whole "system" crashed because of the missing wp. I was building up cargo routes, loaded the savegame and every cargo using autopilot was dancing around because they couldn't find their waypoint :D

Sorry about that, I fixed it as soon as I found out about it.

I have to add that I use your mod quite a lot. Sometimes ONE wp was missing, probably the last I tried to save. Just today EVERYTHING was deleted on startup

It's ok, the Autopilot mod I was relying on doesn't work either. Looks like it's better to reinvent the wheel than to rely on wheel builders.

Lost all my waypoints when I loaded up today. Im so far from home to :(

So not really a Saving issue but this is the closest thing to a bug report forum
So /waypoint add "Test" will work
however /waypoint groupadd "Test" TestGroup" gives me an error
You Do Not Have a Waypoint with the name 'Test' ?

considering that testing with double single and no quotes yielded the same result i have no idea whats going wrong and why the mod cant find the existing waypoint