What a strange error messsage!

I recently encountered a frustrating error while trying to align an .sdlalign file. Midway I did a re-align, only to get the error message:

Some of the passed alignments are complex!

I intially ignored the message and continued manually aligning segments. When I wanted to save my alignment again, the Align program balked and displayed an object-reference error, making it impossible to save my work. My only recourse was to quit Studio and lose what I had done up until then. Very frustrating! The file is not excessively large by any means and contains 2373 segments.

In addition, saving the alignment takes an inordinate amount of time. The file is only 308KB in size.

Thirdly, if I select a server-based TM option as the target for importing the alignment results and click Cancel (because I really wanted to use a file-based TM), I always get the error message about not having an object reference to an instance.

Does anybody have helpful advice?