* Data Recovery Team *
To run the installer with Administrator permissions, instead of double-clicking the Setup program icon, you must do the following:
I ran a trace again to compare the load procedure of the PC with the problem and another similar PC that is working and found that during the startup, the software was trying to load a library file (addinmgr2.dll) which it couldn't find. On checking the file, was in fact located in "C:\Program files (x86)\Common Files\Intuit\Quickbooks". Copied the file to the Intuit program folder which then allowed the software to load correctly. There were some other minor issues like it couldn't run the registration script so obviously all wasn't right and the question remains - why was the file not found in the folder it was installed into.
Further investigation got to the root of the problem which was that many of the registry entries for the Reckon software (and there are many) did not have appropriate permissions. Run a utility to change the owner and permissions which solved everything.
I still don't know how the permissions in the registry were missing but obviously during the first installation attempt, something went wrong with the registry update which didn't update the correct permissions and subsequent attempts to un-install or install would not allow to make changes to those entries in order to fix them. Subsequently the software didn't have read rights to interrogate the registry entries causing it not t find the necessary data to load correctly.