I don't know how much this will help you but it might :)

In your control.lua file line 10, you make use of the script.on_load to check and re-initialize your global variables.

I have been told that using the on_load event is bad for multi-play,
you might want to just remove it and replace with migration scripts,
as this may solve your MP problems.

PS would it be OK with you if I borrowed/stole your icon_sapling.png and used it in one of my MODs?

Next time I have the chance, ill look into whether the on_load event is what is causing the issues, and even if it isn't, migration scripts sound like a much better way to do it, so ill probably change that next update anyway.

It wasn't me that made the sapling icon, but im pretty sure Shrooblord wouldn't mind if you used it if you credited them.