This is a resolved issue, posting it here in case others run into the same issue:

Problem: installed flightpath to a remote server (in this case AWS via Bitnami). It installed OK but css (nice fonts, colors, background etc) did not showing up; after the welcome page only the text shows up. I could click on options, but it wouldn't save them. I suspected it was just not finding the css and tried to make sure in system settings that the classic theme was chosen, and it was, and Clean URLs was enabled. I tried unchecking the Clean URL box but it wouldn't save the setting.

Solution: Following the last line of instructions on this page: http://getflightpath.com/node/5

To disable from the database, should you get "locked out" of your site, you can edit the variables table, and remove the entry for "clean_urls".

Logged into phpmyadmin, went to that table and deleted that entry. Now the whole site is displaying correctly.