I have this entry in the log,  and the new server.prefs file does have the right setting:
[16:08:49.3580] Slim::Utils::Prefs::Base::set (113) setting server::timeFormat to "%H:%M:%S"

note that this is not the default, so it would appear to have migrated.

Is this the only pref that doesn't migrate, or are there others?

Where are your 6.5 prefs, and what type of install procedure was this?  Maybe the installer is creating case where the old prefs are not found?  What is the value for the 6.5 pref?

or, are you instead referring to the datetime screensaver formats?

Yes, I was referring to the date-time screenserver format. This was also reported by someone in the forums.

I'm not sure just at the moment what the original version was: 6.2 I think.

I also lost all my alarm-clock (multi-day) settings. 

datetime prefs for the screensaver did change at some point into a plugin, so prefs from before that may not migrate correctly.  for 6.5 prefs, my test migrated them just fine.  they end up in prefs/plugin/datetime.prefs

alarm prefs should work as well, as these are specifically migrated in Slim::Utils::Prefs.  However, with older upgrade paths, this may also be missed.

Alan: can you dig in and see specifically what items weren't migrated?  

I cannot reproduce this.

This bug is being closed since it was resolved for a version which is now released!  Please download the new version of SqueezeCenter (formerly SlimServer) at http://www.slimdevices.com/su_downloads.html

If you are still seeing this bug, please re-open it and we will consider it for a future release.