Yeah, I've opened a case on it yesterday. I was just trying to come up with workarounds for the meantime. I've asked to have a solution published as well noting the issue and workarounds. I'll reply back here when I get more info from Support.
If installing tools on your Windows host isn't an option, you could also copy the file to LTM, run 'tr -d "\r" < dos.file > unix.file', copy it back to the Windows host and then import it via the GUI. There's probably a way to just import it via the CLI once you remove the carriage returns on LTM, but I didn't delve into that.
Aaron