Re-programming Motorola MCS 2000 Radios

We have been supplied with some MCS2000 radios which where programmed to our needs at the time.
We have now add a new repeater and need to make some changes we have the software but are unable to work out where we have a problem.

When you try and read the radio the display changes to display "CSQ" and after about 10 seconds the radio resets and the software reports "Communication with radio failed".