The profiles are indeed the answer here. They're intended to solve the problem of having to manually change all of your settings each time you want to play a different mod or TC.
When you set up FS2 with regular wxL, you probably used the Default profile. The Diaspora installer adds its own launcher profile, and IIRC the Diaspora 1.0.4 patch adds yet another profile that should be used in place of the original Diaspora profile.
You can check on the Welcome tab which profile you're currently using; it'll be the name that appears in the drop down box under "Profile management".
EDIT:
Looks like the launcher keeps its settings in the registry and it only expects one version of it to be installed
The launcher keeps its settings in your %appdata% folder, which in Windows 7 is probably
C:\Users\<YourUsername>\AppData\Roaming\ . There's just one copy of the data for all versions of the launcher.
The behavior you're seeing is because the Diaspora launcher is loading your profile with your FS2 settings. If you have separate launcher profiles for FS2 and Diaspora, the launchers will still load your most recently used profile when they start up, but then you can just switch profiles on the Welcome tab to get to the other profile.