It turns out that it was slowing down everything else because I didn't have my stored fonts "indexed". Fivos from FMF provided me with the following instructions, and now it's extremely fast when searching my bazillion fonts:
a) Go to menu "Fonts" => "Fontsets setup"
b) Press Ctrl-A to select all fontsets
c) Click on "Create/Update Index" button to create indexes for all your fontsets
When I asked how this makes such a radical difference, he also offered the following:
"Every time you perform a matching the application needs to create some special images of the selected letters (i.e. it renders all fonts and all selected letters).
The index is a permanent store of some of these images for every letter of a font, so there is no need to open every font and this makes the matching super-fast.
Yes, the matching searches all fonts (either with the index or not) and the algorithm results are exactly the same.
(The accuracy and the speed of our proprietary searching algorithm are actually the strongest points of our software)."