Sometimes when I get disconnected my macros will reset and if i am in a party it will not allow me to save the macro even if i am out of combat. It will say "macro saved" but then it will just close the window, and when I open again via /gs it will not show the macro as saved in the list.

Were you in combat and did the OOC queue finish

You can check the queue by looking here. Where it says combat queue is running - if there is anything in the queue it will list here and I have been saving macros both in groups and instances all day.

It said 20 in Queue and this persisted even when leaving the party leaving the instance, being out of combat, and restarting the game. I had to delete the WTF folder and all of my macros to fix it.

no - you needed to wait for the queue to resolve. once that was done it would have been back to normal. Alternatively - you could click on the entries to manually remove the leading ones that blocked your actions