CSI: NY Season 3 Aspect Ratio issue

[Krawk]

Have successfully converted seasons 1 & 2 of CSI: NY (Region 1,) but when doing Season 3 all the resulting mkvs are in a 4:3 aspect ratio rather than 16:9.

[EDIT] Ok so this season is 6 discs and 4 episodes per disc. One single episode on disc 5 saved at the correct aspect ratio, all the others did not.

I can "band-aid" them by using MKV Toolnix and editing the header but using that method creates minor incompatibility issues with certain players or hardware. One thing that no app seems to be able to do after the fact is edit the "aspect ratio" info on the MKV file. You can edit the display resolution but programs such as Handbrake still report a 4:3 aspect ratio.
Can I assume that the aspect ratio is perhaps embedded in the IFO files somewhere rather than the data stream? Does Make MKV not examine the IFOs?

[Krawk]

Creating an MKV using DvdFab seems to also show the correct aspect ratio without the need to modify it afterwards. Is there another header somewhere not being set?