Got a "Path=" statement in your .bat file that points to the correct directory?
What does one of those look like?
P.S. If I hadn't already got my raspi running with my 2pacs and could just add in the BFL part instead of having to install cgminer on the pi all over again then I'd plug it in there lol
One of the lines in your .bat file should look like this:
Path=C:\folder1;D:\folder2
and so on. Make sure your Path statement points to any and all directories with any software, config, etc., that you want to run.
And it needs to be ahead of the command that is calling bfgminer, of course!