Thanks Nee-Elder, I'm submitted a ticket. I worked out it may have something to do with the fact I have two accounts, if after getting this problem I can seem to be able to force a fix by switching to the other account. However, next time after that there is a good chance it will return.
I would normally first do a repair with the launcher, but that option is always greyed out. I've download the (direct) launcher again and did the repair use in the setup exe. After logging it, it's now doing a 38GB log download.. AND, it's installing the files to a different directory, WTF!
At this stage I'm assuming support will just tell me to reinstall (the 3rd time in the last couple of months).