As an update to this it seems to only be affecting regions 1 and 2. Regions 3 and 4 go directly to the bottom quarters of the screen as expected so I'm going to delete the ini file and redo it tonight to see if there may be a hidden region somewhere in there. Will let you know how it goes.

[EDIT]

Sorry, forgot to add an answer to your questions.

Compatability mode is unchecked
Advanced text services I'll have to recheck when I get home.