It seems to be an ongoing issue and I haven't heard anyone offer a solid solution yet nor have I seen anyone from the UO team even acknowledge that it is a problem. And yet many of us have posted about it!
Something else that I think may be somewhat tied into this issue involves the Crystal Ball of Knowledge. I have been using one with my fisherwoman and noticed that it had unexpectedly turned itself off one morning, even though I have never touched the thing since turning it on in that character's backpack several weeks ago. The only thing I could think of that could have caused it to become turned off was logging onto the same character on my husband's computer one day (something I usually don't do and possibly had never done before with that particular character) and then later on logging onto that character on my own computer. That was the point at which I noticed the Crystal Ball was no longer working and was in fact turned off. So where/how did the game get the instruction to turn off the Crystal Ball when I used a different computer and never even clicked on the Crystal Ball? Similarly, why does the game on any particular day just deselect the option to run the mouse in a separate thread for a random character? And when this does happen, why does it often seem to affect only characters on a particular shard (e.g., last time it happened repeatedly, it seemed to be happening with characters I had on Napa)?
It would be very helpful if one of the engineers could give us more information about the character configuration files used by the two clients. What I would really like to know is: (1) what is controlled by these files (i.e., are things like the mouse setting and the Crystal Ball setting even controlled in these files?); (2) which file(s) the game uses as a default source for character settings if it cannot find a character's configuration file at all or cannot find a setting for something in a character's configuration file, especially when you have multiple accounts and they aren't all updated to the same expansions, you play on multiple shards, and sometimes have characters with the same name on the same shard or on multiple shards; and (3) what we as players can safely and legitimately modify in the character files to avoid these types of annoying situations in the future.
There is some very basic information in the official Knowledgebase about character settings. However, some of the information (e.g., where the character setting files are located) is out of date and neither article addresses the setting for running your mouse in a separate thread or touches on newer items such as the Crystal Ball of Knowledge:
http://support.ea.com/cgi-bin/ea.cfg/php/enduser/std_adp.php?p_faqid=10467
http://support.ea.com/cgi-bin/ea.cfg/php/enduser/std_adp.php?p_faqid=276