John,
I'm not sure which radio you have. I have the vx5r, and I had no trouble
cloning the template from the radio to the computer using JFW. If you're
losing data in the radio, then you must somehow be writing to the radio
instead of reading from it.
I hope it doesn't sound like I'm stating the obvious, but I mention it only
because I know it can be confusing.
Good luck.