I received your PM, but I don't see anything funny there. Not sure why one subject would be different, but some ideas to check.

1. Check the '\' end of line characters. Any spaces after the line continuation character will generate an error. Try using Rick Reynold's file_tool to check for that with something like this on your script.

file_tool -infile MVM.txt -show_bad_backslash -prefix MVM.fixed.txt

2. Another odd problem that we have seen just recently also concerns the line continuation character. On some systems' tcsh shells, there may need to be at least an indenting space on the continued line. Your lines aren't indented in what you sent, so that might be an issue.

3. Try using the wildcard expansion (globbing) by 3dttest++. The help shows how to use this for the short form by enclosing everything in single quotes. That's a bit trickier to do with the variables, but it is possible.
3dttest++ -setA '*.beta+tlrc.HEAD[Vrel#0_Coef]' \
-setB '*.beta+tlrc.HEAD[Arel#0_Coef]' -prefix VAtest -paired

4. Paths for each of the files can often be quite long, so you may have run out of character limits for the input buffers for the shell. We usually don't run into this problem, but it's possible, particularly for older systems. You can check with :

getconf ARG_MAX

You may be able to alleviate some of this by creating symbolic links with short names to each of these directories and use those in your script.

5. Finally try this on the command line with no variables and just that misfit subject and then maybe a few more. If that subject continues to be an issue, narrow down on it some more by repeating in that subject's directory without any path in the command. Check specifically for problems with extra spaces in the names.