Yes, I could reproduce the problem with that theme.
It seems that wordpress generates a single request to load all dependencies for various javascript files, and if a theme includes a lot of them, this request will get longer than 255 characters, which is the commonly used maximum for file name length on most filesystems. It looks like your plugin is just taking the request string and saving a file under that name, so if the request URL get’s too long, we’re not able to save it.
Hope this contains some helpful information for you.
Best regards,
Ben
We use it in multisite environment, and it works for us, except with a problem generating JavaScript when lots of dependencies are involved. I already opened a thread to that issue.