HAWAIIAN STARMAN  Same crash here. I posted a crash report at the developer's site.  
(Version 2.7b15)

HAWAIIAN STARMAN  v .41 recreates the "favorites" problem with Glims, i.e. on the restart after Safari Cookies install, all favorites are unchecked. By contrast, v 4 corrected the bug. Seems like a step backward.

Had to revert to v .4, and also reestablish my Safari Preferences from an earlier version of com.apple.safari.plist to reestablish my favorites - again!  
(Version 0.4.1)

HAWAIIAN STARMAN  v .4 fixes earlier problem with favorites and other minor issues. Great to see the import/export option.

Well done!  
(Version 0.4)

HAWAIIAN STARMAN  Glims developer sees problems in Safari Cookies code causing the lost of favorites when Glims is installed. Developers are talking.  
(Version 0.3)

HAWAIIAN STARMAN  Thanks. I figured it out via trial/error. Would be nice to have better documentation about how cookies are managed behind the GUI.

Seems when I installed the latest version of Glims (v 16) i the preference file was altered, perhaps affecting the cookies favorite information (assumption on my part, however, that's the only change I made which would have impacted Safari's preference file).

Restoring an older version of preferences (gotta love Time Machine) reestablished the favorites. I'll send notice to Glims' developers.  
(Version 0.3)

HAWAIIAN STARMAN  Until today, Safari Cookies (thru v 3) worked pretty well. However, after a Safari restart all of the favorites selected (119) have reverted to a non-favorite status.

I'm using Safari 4 Beta on an Intel Mac 10.5.6. Rather daunting to recreate the favorites. I have Time Machine operating. What file do I restore to recover the favorites without having to recreate the entire list? The only change was installing a beta version of Glims (v 16).

As an aside, I notice at times cookies reappear that seemingly were removed.  
(Version 0.3)