That's a pretty good article on iTunes deployment.
I've never had an issue running a .bat file from the 'Command Line' of a SCCM program. Perhaps using .bat instead of .cmd will help solve your issue.
'Program: iTunes 9.2 Update succeeded with exit code 0' seems to indicate that the SCCM client was able to download and execute the file. In the windows-noob.com BAT example the code always returns '0' (that's what 'exit 0' does). So, even if one of the MSIs fail the BAT file will always return a 'success' message to the SCCM client.
This is a tricky issue and the only way I've been able to look into the issues is to log all of the MSI installs.
For example "msiexec /i iTunes9.1.1.12.msi /qn /norestart /log c:\isdept\iTunes9.1.1.12.log" will create a log file when the MSI is installed.
Also,
UserContext = "NT AUTHORITY\\SYSTEM"; implies that the SCCM client is executing the bat/cmd file as the local system user. It is unlikely that this user has access to the files if they are on a UNC path (as the windows-noob.com article suggests).