Yeah I just had this kill me again. I fixed the issue for now though. All 5 of my wow folders are separate but I also have a separate 6th folder with max addons/settings for single boxing using the same account as my Wow1 multiboxing folder. I logged onto one of my singlebox characters last night and then logged back into my multibox character and my main lost all his general macros again.

Solved the problem by retrieving the macros-cache.txt file from backup, and then copying it to BOTH account folders in both wow folders - this will solve the problem but any time I add a new general macro I'll have to copy the file again