Ok, so here's a bug waiting to happen, the options page for the Domain Mapping plugin uses the function
add_site_option to save options, which is lazily used to add AND update options, however as of 3.3 it will now only add options as originally intended, and will not overwrite any existing options.
You can see a brief explanation of this being introduced in 3.3 in
add_site_option's Codex page:
I guess this will hit a lot of plugins.