I solved this issue. It's an inelegant solution, but it's working as expected.
Here's what I did:
1. get a copy of the Get Recent Comments plugin.
2. make a copy of it
3. open the get-recent-comments.php and carefully edit each use of the following expressions:
get-recent-comments
get_recent_comments
get_recent_trackbacks
Recent Comments
kjgrc_
change these to read:
get-recent-comments2
get_recent_comments2
get_recent_trackbacks2
Recent Comments 2
kjgrc2_
Now be sure you change the name of the folder to "Get Recent Comments 2" or whatever you want, and the name of the "get-recent-comments.php" or whatever you want.
Load this into your plugins folder and activate it.
If you get an error, note what the error is, and this will usually tell you where you missed a duplicate name, function, or other registered piece of the plugin (go in and correct it) or that you have bungled it completely and should start over.
Now call this plugin with this call:
<?php if (function_exists('get_recent_comments2')) : ?>
<?php get_recent_comments2(); ?>
<?php endif; ?>
Now go into the admin settings, and exclude the categories you want off this second list and update your settings.
I've repeated this for the four categories I display on my index, so I've got four lovely little lists of single categories, and the corresponding comments below.
It's cumbersome, but it's working!