Hi Sergio,
While it's good that you found the way around the issue, the "Best Practice" way is probably worth troubleshooting still.
Basically, what you'll want to do is:
1. Create a logfile:
msiexec.exe /i package.msi /l*v c:\install.log
2. Look at the property dump at the end of the log. Specifically, these properties should have a value of '1':
ARPNOMODIFY
ARPNOREMOVE
ARPNOREPAIR
If these are not set, your transform either isn't getting applied, or it doesn't contain the entries you thought it does.
Regards,
Cary