I was finally able to migrate my meta-data updates on picklist values on the standard objects such as 'Leads', 'Contacts' etc. by doing
a 'Deploy to Server' when selecting objects and right clicking on them and choosing 'Deploy to Server' from the 'force.com' menu.
- I do believe that @Mike Chale had a good point that the errors I was experiencing, from just refresh was due to time stamps on meta data differences between my local copy and that of the production server.
So after taking some initial precautions in backing up data and testing 'Deploy to Server' on non critical objects and the sandbox, I overcame my fear and proceeded to deploy to production.
Also this takes a degree of patience as the IDE has to run through a series of debug tests against 'Referenced Packages' but this is just standard, and then generates a debug and deployment log. The deployment log is good as it will actually name the meta data objects you deployed and describe success or failure, it also updates the entire package.xml that describes only the objects you updated.