I just started having this problem too... so i just made 2 seperate FS2 installs... i just copied my FS2 folder with all the SCP material to my desktop for backup, then just reinstalled the Retail version to play R1. Hopefully this mission works now... It sucks though... cause now the graphics look like ****....

Just one question though... Anyone know how to get Text-to-Speech to work in retail? how can you do it without the SCP launcher?
EDIT: And now my afterburners dont work... WTF??