I'd assume you have.. but be sure you update to 0.3.0309.1 since there was an issue with generating the codeplug using the "Write to Radio" buttons.. where it wouldn't actually generate the new codeplug correctly, so anything new you added since reading from the radio or opening a codeplug would not be written..
"Save" and "SaveAs" would work correctly, so saving and then opening the codeplug file then writing it would work fine. However that was fixed in the latest version (0.3.0309.1)
How many contacts do you have?
Current firmware will only allow 255 contacts, closer to about 232 before issues start.
I believe you can have 2000 contacts in your contact list just fine but if you try to set the channel contact to any contact >255 then it will break and you'll see "no contact" on that channel.
As for the "Unprogrammed"
I'm not sure why it would display that, if the zones were written to the radio correctly.
Two things:
Send me the JSON file and I'll write it to my radio through the debugger, where I can see that data that's being written and see if there's an issue there.
also
Download a binary codeplug from your radio and send be the .bin file that it saves, that is the RAW data from the radio before being converted into the readable codeplug.
Maybe I can see in that why it would show as unprogrammed.
To download the binary:
Right click the "Read From Radio" button on the toolbar, you should see the menu for it.
Click that button, it will download the codeplug as normal but then prompt you to save it as a .bin file. Send me that file.
bin.PNG
You can attach them to a post here, or if you wish to keep it private.. PM them to me on here, or on Facebook (if it will allow, maybe zip them)