Does gqcam just generate a file intermittently? Then I don't see how ftp would interfere with it. You need to narrow down the problem, take out the ftp and see what happens if you just sleep in a loop. Maybe gqcam is not getting some environment variable or argument it needs?

Or does it spawn some GUI and generate files as a side effect? Then I'd run it as an entirely separate process and the ftp script as another process. I might do that anyway.