thanks for the suggestions Jan,
I do use absolute paths in my scripts so it shouldn't be that.
I'd also tried running the scripts in the background and that hadn't helped either.
As to your suggestion, I'd prefer to initiate the sync from the kindle as the remote server is outside my nat'ed network and would require opening and forwarding ports which i'd rather not unless I have to. Especially as pulling from the kindle
should be relatively simple

thanks for the help though!