what does "fixing permissions" do in the ROM Manager?
I believe it does a chmod to all files/directories and sets the read/write/execute permissions to whatever the author has determined are the correct permission settings for the system files.
I read somewhere else that running the "fix permissions" option will often fix force close errors that you might be receiving but I didn't see anyone confirm this. The few times I've run it, I found that all of the apps I disabled using SystemApp Remover (great app!). When you click the Disable option for an app in SystemApp Remover, I believe that it's simply setting the permissions on the apk file so that the app cannot be run. Running the fix permissions option from any other app resets all files, including the disabled apps, back to factory default, hence they show back up in your app list and can be run again. I then needed to disable all the apps again.