Well, after more testing, here is what I've found:
I got the game to play back a video-only ROQ perfectly, but if I add an audio track to the ROQ the game throws up - although the video content will still play, the audio track is recognizable but somewhat garbled and slightly detuned, and once the video stops playing the game outputs no sound whatsoever until the game is exited (back to desktop) and restarted.
I did some research on audio in ROQs, and yes, I properly encoded the audio at 22KHz, and VLC plays it back without any issues now, but the game still doesn't handle the audio part properly.
I tried switchblade both v4 and v3 for encoding the soundtrack. I also tried pre-encoding the soundtrack at 22KHz so switchblade wouldn't have to convert anything, yet still the game only plays the visual part properly, sound garbled. (VLC media player still plays both audio and video fine.)
I noticed that the game has an older version of the SDL.dll compared to the SDL.dll that comes with switchblade, I don't know if that makes any difference or not.
I also went to the game's config menu and changed the audio settings before firing up the ROQ, it didn't help.
If anyone can offer any further suggestions to try (or point out something if I'm forgetting something stupidly) please let me know.
I'm also going to re-try a few more things, if I still can't get it to work I'll just put the ROQ up for download with a link here so other people can try it. I'm also going to try it under Kubuntu and another computer to see if that makes any difference.
I tried these experiments with both the 2.2 main release and the 2.3 development release, same results: perfect video, garbled sound, then no sound at all playing the game after the video is stopped.