No I hadn't encoded the .vob files at that stage, they were ripped straight to my hard drive. I don't think they are apart of the actual video steam either, because subrip found the subtitles.
By the way, there are a lot more subtitles than I had thought!
I tried using subrip like Chickenman suggested. I used the OCR option (can't remember if that is the name? I'm not at my PC), It found all the subtitles, and I saved them to an .srt file.
Then I ripped the .vob files with only the video and sound streams, and ran DVD2SVCD, and included the external subtitles, however 17hrs later (slow PC) I played the mpeg files with Windows Media Player 6.4, and no subtitles!!!
When I ran DVD2SVCD I choose 'SVCD Subtitles' under the Subtitle tab, should I have choosen Permanent?