It sounds like the ePO server believes that the master repository is in use. Try this:
1) Stop all three ePO services.
2) Open ..\<ePO install folder>\DB\Software\sitestat.xml in a text editor.
3) Check the SiteStatus value: the status should be set to Enabled. If it's set to Disabled, change it to Enabled, and save the file.
4) Start the services again.
If I'm right you should be able to check packages in again.
I'll give that a try Joe, thanks. Think I did have a go at setting it to Enabled, but probably missed out the stopping of the services bit!