I guess the indexmenu settings are not in a simple text file that I could edit?
conf/local.php
what do I loose by cleaning out the cache, because I already tried that, and it did not change anything?
You lose only the extra processing time needed to reconfigure the cache.
I think you are over-analyzing the problem. If you want to disable indexmenu, then do as I've suggested:
$plugins[indexmenu'] = 0; Then you can go to the extension manager and reinstall. This will over-write your css, where the problem seems to be coming from. But backup and then make the other changes as also suggested.
Would not cleaning up Meta Data have caused this problem? (i could still do it)
The meta files contain data used for the functioning of the wiki but not, I believe, the css. And if you are thinking of doing this, I would leave the meta data alone.