Is the removal of macros working? When I try to remove any macros using the UI window, all other macros show up as nil. If I try it using command line, /ihml list no longer works. If I reload UI, the one I'm trying to delete comes back again.
I can not reproduce this. Deleting macros is working for me and they stay gone when I reload UI.
Try delete (or just rename to backup) the IHML.lua in your WTF/Account/<Account name>/SavedVariables folder.
If that doesn't fix it try disable all other addons to see if there's any other addon interfering.
If you find out what was causing it or if anyone else is experiencing this problem I'd love to get more info so I might be able to fix it.