I posted a similar message over on the Wordpress.org forums about this but the problem seems to affect my MU installation and not stand alone blogs. Here is the problem:
I have a plugin that uses NTLM to authenticate the user. This part of the plugin seems to work just fine on stand along blogs. I can't test it in MU because when I activate the plugin, I need to set some options for the plugin. While this plugin is active, I can not save options on any plugin, including this one. The form post always comes back blank. If I disable this plugin it still causes this issue until I close the browser and reopen it. This one has me stumped.
I am using MU 1.5.1 right now as we need to use the WPDirAuth plugin which seems stable only in that version. Besides that, I can disable all other plugins and the problem persists. I have to assume it is something with the NTLM authentication which sends headers if the user is not yet authenticated. Perhaps the post variables are lost there, any thoughts?