You know, I had this same issue last night. My problem probably isn't the same as yours, but I did notice that in the mod.ini file it listed several directories it needed to function properly. You see, I had my 3.6.12 mediavps folder named 'mediavps_3612', whereas ST:R was looking for it under the name 'mediavps'. A quick rename of my mediavps_3612 folder to mediavps resolved all the issues.
Go into the ST:R mod folder, open up mod.ini and take a look at what other mod directories it lists as a requirement, and make sure you have those in place in your Freespace 2 directory. From memory I think it needs the original Freespace Port, Silent Threat and the MediaVPs.
That's the only advice I can really offer sorry, as that's what was happening in my case.
*edit* I see from some other postings in this section that everyone's recommending you keep a 3.6.10 MediaVP install in a folder just called 'mediavps' and a 3.6.12 version under 'mediavps_3612', to retain compatibility with certain mods. In my case, I had my 3.6.10 install folder labelled 'mediavps_3610' and my 3.6.12 folder labelled 'mediavps_3612', so that would have been MY main problem. Regardless, renaming my 3.6.12 install to 'mediavps' got ST:R working beautifully for the time being, and there's nothing stopping you from just changing it back when you're done playing it to avoid any problems with other mods...
Hope this isn't confusing for you!
