After migration dock only shows when secondary monitor is mirroring, but only for the migrated profile

We recently migrated a laptop user from a 2011 Macbook Pro with OSX 10.8.5 installed to a new 2015 model with 10.11.1 (El Capitan). For this migrated user the Dock will only show when a secondary monitor is plugged in via a thunderbolt adapter and mirroring is enabled. It will not show when mirroring is disabled, or when the secondary monitor is unplugged.

As a further interesting note, some windows cannot be closed by the red/yellow/green buttons at the top left of the window (brings up the "beach ball of death" for a short while). Windows close/minimise as soon as the secondary monitor is plugged back in.

I've deleted the com.apple.dock.* files under the Library directory, but this hasn't resolved anything yet.

The interesting thing is that when a "new" profile is created it works perfectly. Switching to a new profile may be the only solution, but will require migrating a lot of things like Parallels across.