D'oh! I've created a home grown plugin/theme combo, and upgrading to wordpress-mu-2.6 exposes a bug which causes my options to duplicate on some blogs, with the 2nd option populating with the defaults. At first I thought I lost data, but upon analyzing the database, I could see that the options are just duplicated.
Here's how they were called:
add_option('freedom_sitedomainsub', 'www.','Sub domain value--useful if subdomain is different from http://www.','';);
In troubleshooting, I removed the description and set autoload to 'yes':
add_option('freedom_sitedomainsub', 'www.','Sub domain value--useful if subdomain is different from http://www.','';);
Finally, I've changed it to this, since the optional description has been deprecated, and I don't care about autoload:
update_option('freedom_sitedomainsub', 'www.');
my data before loading in wpmu 2.6 shows:
73, 0, freedom_sitedomainsub, 'www.', ''
after loading in wpmu-2.6 it shows:
73, 0, freedom_sitedomainsub, 'www.', ''
14567, 0, freedom_sitedomainsub, 'www.', 'yes'
Any ideas?