
I was able to find the source of my problem and fix it, sort of. I'll describe my solution, just in case anyone else is searching for a solution to this problem. Or if anyone has a better solution, please let me know.
I am running a module called Mantis. Search results kicked out by Mantis were being written above my theme. I found a suggestion here that showed me how to remove a module form the Search engine by editing the xoops_version.php within the Mantis module folder.
I found the following code:
// Search
$modversion['hasSearch'] = 1;
$modversion['search']['file'] = "include/search.inc.php";
$modversion['search']['func'] = "mantis_search";
and changed it to:
// Search
[b]$modversion['hasSearch'] = 0;[/b]
$modversion['search']['file'] = "include/search.inc.php";
$modversion['search']['func'] = "mantis_search";
This removed Matis results from my global search. Fortunately I don't need them.