I had a baffling issue with the excellent Zone Manager utility programming my CS700 codeplug.
It's a long story, but I was using Contact Manager, Zone Manager and Channel Manager To get my codeplug up to date. Channel Manager requires a 'blank' codeplug with only one channel in it. You create the 'blank' by deleting all the channel but one and re-saving the codeplug to use as a template. When I used Zone Manager to manage my 'blank' codeplug and although Zone Manager would manipulate the zone order, save OK and reload the saved codeplug and show all the zones, opening the codeplug in CPS 1.25 (for the CS700) would only show the first few zones.
However, when I used Zone Manager on the codeplug with all my channels imported using Channel Manager and contacts added with Contact Manager, everything worked as advertised with Zone Manager working as expected.
I can only assume that I'd 'broken' something deleting all the channels but one to create my template for Channel Manager.