Quickbooks 2012 Pro with Mar 2012 update on Windows 7 Ultimate with SP1 and all updates to March 2012 including IE9 and .NET 4.0 Full.
Intuit's support article SLN55044 hints at the solution I needed:
I had to use regedit to add the iexplore.exe key with default and path values to HKEY_LOCAL_MACHINE\SOFTWARE\Wow6432Node\Microsoft\Windows\CurrentVersion\App Paths\IEXPLORE.EXE.
You can copy the ones from:
Why Intuit don't just come out with this...
I think it may have been because I installed Opera.