I've run into a problem with specifying multiple CIA files in different directories for a BART run. Note that this does not cause an error when running Transit by itself.
If I have one CIA file in some other directory and a second CIA file in the directory that I am running BART from and specify the path as ./secondCIAfile, BART throws an error that it is unable to read the second cross-section file.
If I specify it as ../another directory/filename, it also throws the error. From the error I see that it is looking in the directory of the first CIA file and is ignoring the relative path that I have given it. However, if I give it an absolute path, then it works. If both CIA files are in the same directory, then it also works.