So, how about sending the problem SDL TM file to the CT support desk for analysis. I think they can give you some advice.
It is on my to-do list. Do you know what Trados version the sdltm file was created with?
The misalignment issue seems to occur when one of the segments in the sdltm file is corrupted. Then from that segment on, the misalignment appears. I will see if CT is able to repair or ignore such a segment. For now, please request your client for a TMX file in such cases.
Yet another example where developers of other CAT tools have to program around shortcomings in SDL products. Just like the invalid XML characters in their SDLXLIFF files.