It seems to me that all subtitles made with Aegisub v2.1.2 RELEASE PREVIEW (SVN r1987, amz) do not work with mediacoder. You can see the subs in the preview, but when trying to put them onto video it doesnt work.
An early version, 1.10 works with mediacoder so i figure this must be the problem.
I am currently using Vista so i cant say if this is the same with XP, however i did try it on an xp based comp and it still did not work.
If i can help developers in any way at all, just let me know ok.