Hi,
I checked my Main Messages window by starting a New Message and typing the first two letters on my name in the "To" spot.
It then lists various options for AIM, Jabber, Yahoo and iMessages IDs and Phone numbers based on Address Cards from my three computers
It showed my Landline number with the +44 for Great Britain (and the dropped leading 0) which is not the version on the Address Card it was quoting.
(Messages thinks any phone number is a potential iMessages contact point).
For me this is working.
An example I can post of a UK vehicle supprt service

It does not go red until you select it as the "Contact" (which I did to separate it out from the other ones starting "ra")
At this stage it is unclear if it is the Contacts app that is not supplying the Messages app with the correct info or whether Messages is not using the Info correctly.
For Messages this woiud be in the com.apple.ichat.plist file
I can only see this item

From that info it is unclear what the function is .
The Column Offset could be the amount right the drop list of potential contacts are from the "To" spot.
Deleting com.apple.ichat.plist will remove any Preferences Settings (apart from Accounts) that you have changed in the Messages Preferences.
This includes the Viewing Choices regarding Colours and Fonts and so on.
I am unsure of other apps and deleting their .plists
Generally this can be less invasive than a complete reinstall/recovery of the OS.
I would consider Repairing Permissions. (Applications/Utilities > Disk Utility > First Aid tab. > Repair Permissions button)
And possibly redoing the Update.

9:44 pm Friday; February 28, 2014
iMac 2.5Ghz i5 2011 (Mavericks 10.9)
G4/1GhzDual MDD (Leopard 10.5.8)
MacBookPro 2Gb (Snow Leopard 10.6.8)
Mac OS X (10.6.8),
Couple of iPhones and an iPad