I feel like this is a relatively basic question, but a solution seems to be beyond my Google-fu.
Ahah! Fixed it.
To anyone who had a similar problem, the problem was indeed with the @ symbols. I was using the AFS file system, which resolves @sys in a filepath to the machine/operating system pair. There there were '@sys' strings in my paths to keep it general-purpose, which MATLAB saw and misread as the keyword to denote a class folder.
I replaced all occurrences of '@sys' with the actual folder name, and MATLAB parsed them correctly. Note that this solution was not immediately obvious because the path I was using was a symbolic link to the full path with the '@sys' strings.