Not even sure how I found the reason: mime type of *.r files (plain text R scripts) got set to "application/x-extension-r". (by ~/.local/share/mime/packages/user-extension-r.xml) . I checked update logs but couldn't determine the origin of this file. Interestingly, that happened only on one of two similar installations with the same 64bit Fedora 11.

Any idea which program could have done this?

My solution was to put in ~/.local/share/mime/packages/Override.xml the following:

<?xml version="1.0" encoding="UTF-8"?>
<mime-info xmlns="">
<mime-type type="text/plain">
        <comment>R script; somehow was application/x-extension-r</comment>
        <glob pattern="*.r"/>
Then run:
update-mime-database ~/.local/share/mime
That fixes it for tracker; for beagle, also needed to remove