Aktan is one of the few encoders of PCSX-rr. The reason is the encodes of this emulator must be doned with Eternal SPU Plugin, the best sound plugin. Unfortunately, there is an issue: This plugin cause desyncs in the movie file. The process to make it sync is tedious and takes a lot of time to accomplish it.
That being said, I don't recommend you doing your own encode, which will obviously sounds bad due to the sound glitches of TAS Sound Plugin.
EDIT: The process is this:
1. Check "Show FPS display on startup" in the TAS Graphic Plugin.
2. Set the sound plugin to TAS Sound.
3. Record the whole movie with regular .kkapture without sound.
4. Set the sound plugin to Eternal SPU 1.41.
5. Make sure the settings in Eternal SPU are SPUasync, async mode wait, buffer size 12.
6. Use this version of .kkapture for Eternal SPU captures and make sure "Skip frames on frequent timer checks" is check and that the frame rate is set to 120.0:
http://www.mediafire.com/download.php?oq4491c34o373nh
7. Capture until first desync without sound.
8. Compare the TAS sound capture with the Eternal SPU capture carefully to find the exact first frame it desyncs.
9. Look at the in game frame number (this is why display is on) and subtract 24 from it.
10. Play back the run in PCSX-RR with TAS Sound until you get to that frame and then save state on that frame.
11. Switch to Eternal SPU and capture the run without sound, but this time load the save state you made in step 10.
12. If Eternal SPU capture now passes the desync spot, capture until the next desync and repeat from step 8. If there is no more desync, proceed to step 13. If it still desyncs in the same spot, proceed back to step 9 and try subtracting one less than you did last time (aka try 23, if still doesn't work, try 22, if still doesn't work, try 21, etc...).
13. Now that you have all the save states (I hope you have a different save state for each desync), capture the run again with Eternal SPU with sound and "Show FPS display on startup" unchecked in TAS Graphic plugin for all save states.
14. Combine the parts and remove the extra junk between each part and you finally have a complete capture.