System info:
OSX 10.8.3
Alfred 2.0.3(187)
Reproducable: Yes
Steps to reproduce:
Duplicate a theme, naming it Keep it selected. Close Alfred Preferences through cmd+Q or clicking the red x. Use Alfred hotkey to bring up Alfred window. Press cmd+p to bring up Alfred Preferences which should start on the Appearances panel. All custom/imported themes are gone leaving only the defaults of which the first is now selected.
Additionally my Appearance Options were:
[x] Hide hat on Alfred window
[x] Hide prefs cog
[ ] Hide result subtext
[ ] Hide result shortcuts
[x] Hide menu bar icon
They now are all deselected, but continue to behave as if they were selected as above.