Vector NTI/AlignX format: converting to MSF problem

See data from UGENE-6031.

There is a problem exporting the data into the MSF format:

1. Open the*.apr file in UGENE.
2. Select "Convert to another format", set format to "MSF", click "OK".
   Current state: In 1.29 the file is not opened with an error:

      Check sum test failedDocument was removed
      

   In a snapshot version the opened alignment in MSF format contains only some sequences. There is a bunch of errors in the log like:

    
      Unexpected check sum in the row number N
      

   Expected state: Open the document without errors. Note that there is no problems with converting the data into FASTA or ClustalW format.