Well... actually... What you state as 'doubtful' is exactly what happened.
Also, the uploading of files and the methodology in which the phpBB/Perl worm propogated were not related. The phpBB worm 'Santy' worked by injecting the Perl code directly in the URL of the viewtopic.php script. The other 'issue' was related to the failure to sanitize all the form variables on the an input form allowing script to be pushed into the PHP context.
http://www.securityfocus.com/archive/1/385063
This (like all SQL Injection and buffer overflow vulnerabilities) is an input sanitizing and validation issue and a direct reflection on secure coding practices of the developer.
Today, phpBB is quite well hardened against SQL injections. At least the current version. But... EVERY new version need to be carefully scrutinized as these things tend to creep back into production code.