Not sure why they would not be captured consistently--like I've said, the transform wizard hooks the property table, and if they change, it should be captured in the transform.
Do you see that it's inconsistently capturing the 'Uncheck' action you're doing? Because this is something I've not tested--this would undefine the property in the property table, rather than changing the value. I'd be interested to see if this was the case.
Can you post an uncompressed copy of the *.msi package? This can be done by using the following command:
msiexec.exe /a package.msi
