I'm using your lovely plugin on the twentyeleven them - looks great, except I only ever see 5 entries posted. Here's my shortcode:
[mctagmap columns="3" num_show="20" more="more »" toggle="« less" show_empty="yes" tag_count="no" width="170" equal="yes" from_category = 15 ]
I figure this is something to do with me using the 'from_category' option, and the notes you've put under the 'theme addition' heading in the install docs, but I sadly don't know what that code is trying to do. I did try pasting that into my tag.php in a few places, but it didn't seem to make any difference.
I know you've said you cannot support specific themes - but can you give any hints on what that PHP is trying to do or what problem it is fixing?