I found that editing the intall.msi with ORCA and adding a row for PIDKEY in the Properties table pre-populated the key into the required fields and allowed the install to proceed silently without any problem.
I used a Group Policy to populate the users AppData folder with the licenceData.jlp file needed for the program to operate without installing as each user. This puts the file in c:\users\%username%\AppData\Roaming\Jolly Learning\licenseData.jlp