I have seen a few Configuration Manager R3 installations failing when trying to create the Configuration Manager package and program. To fix that problem I extract the SCCM2007-SP2-KB977384-ENU.msi file like this:
msiexec /a SCCM2007-SP2-KB977384-ENU.msi /qb TARGETDIR=D:\R3
The command will extract all files and place them in D:\R3. From this folder you can take the sccm2007ac-sp2-kb977384-x86-enu.msp file and create the configuration manager package manually.