This is what I discovered today (with the last build and the build before) with a mqxliff file:
The A's are missing. I never saw this before, and with any 100 % match this does not happen.
I am not sure but perhaps your (third-party?) TMX memory may contain some tags in the source segments that prevent the proper display of some characters in CafeTran's html-based viewer. You may submit a support ticket and attach the TMX file if it is not too large.
Possible, but not all necessary solutions: