We've started uploading TAoC mod through the FTP now and so far, haven't had any issues. Had no clue as to HOW to do that but once I figured it out, it's actually pretty easy to do. Only thing is, it takes MUCH longer to install/update mods that way it seems. My buddy (the server owner) and I are really new at all this but we're figuring it out as we go.
I am having the exact same problem. After every auto restart, the server stops detecting Age of Calamitous. It also did this a few days ago with Pippi but after a few hours it started detecting Pippi again. Then as of last night it did it with AoC and not has just done it again.