Matrix encoding finishes early (FlaskMPEG)

[Manga Man]

I'm using FlaskMPEG 0.6 and trying to encode my Matrix DVD into Divx 4.12. The only problem is, when I load the IFO file in it only recognises the first 2 hours of the file (4844 MB), and leaves off the last 11 minutes. When I scan to the end of the file, this is true also but, if I then press play it will keep going to the end of the movie. If I set my mark out pointers after having searched past the 2 hour limit and begin encoding, the process states that it will take over 106 hours!! Instead of the usual 5. Either way, if I try the 'compile whole file' option, it only encodes 2 hours of the file.

Is anyone having similar problems or does anyone know what I am doing wrong? I'd appreciate any help, thanks.