In case anyone stumbles across this in the future - we finally managed to find a solution to this.
This issue was being caused by the Regional Settings on our server (Windows Server 2012 R2). For some reason with the fresh install it set the decimal symbol as a ',' (comma) and the list separator as a ';' (semi-colon).
Can be changed as follows:
On the server, go to Regional Settings - from the start page, type 'region'.
Click on 'Additional settings...'
In the following window, change the fields to your required settings:
It might also be an idea to change the Currency settings in the relevant tab.
If this doesn't work - which ours didn't - settings can be changed in the registry:
Note that above is changing for the default user - it might be necessary to change the registry settings for other users on the server - most importantly the user which runs the QlikView services.
Best of luck!