Easy... you have to tell FRED which mod to use. In this case, FSPort & mediavps. So, do this:
"c:\games\freespace2\FRED2_Open_3_6_9.exe" -mod fsport, mediavps -fredhtl
The -fredhtl needs to be last. The -mod fsport, mediavps tells it to use fsport primarily, and whatever it can't find there, to find in mediavps, and after that it will find stuff in normal FS2 directories. Do you understand now? FS2_Open .exe does the same thing, but the Launcher does it for you to make it easy, using the "select MOD" feature.