There seems to be a problem with the iconcache.dat file in the most recent Beta versions. If a page is reloaded, sometimes the right favicon is not picked.
To get your favicons back, you can try deleting (or renaming) the iconcache.dat file, and see if your missing icons are not restored one by one.
Windows XP Pro SP3 | K-Meleon 1.6.0 Beta2
Trying out various subspecies of the lizard