A PSA for those of you using macro apps like SoundFlow:
If Matchbox is failing to reconform Pro Tools correctly, it may be the case that your macro app is hijacking important keyboard commands fundamental to normal operation of Pro Tools.
SoundFlow in particular, seems to have some default macro set which swallows the /Slash key, and this is obviously pretty important for Matchbox to be able to enter the timecode in/out fields.
So please make sure that this specific macro is disabled and keep an eye out for any others which might affect Matchbox.