However a quick investigation turned up the cause of the issue. As of patch 5.4 WoW no-longer seems to respect the run in 32bit mode option Pwnboxer sends to it (something Pwnboxer currently needs it to do).
Rather it looks at your OS and goes 'oh this is a 64bit pc I'll use the 64bit client' even though it has been asked to run the 32bit client.
The fix to this however is quite simple first go to the 'WTF' directory under the wow directory and look for the 'Config.wtf' file, then add/amend the line below
SET launchThirtyTwoBitClient "1"
Then go to the main wow directory and rename the 64bit client from 'Wow-64.exe' to 'aWow-64.exe' that will stop the launcher trying to load it.
For more info, see the official forum post about the problem