The reason for the huge increase in PHP is that PHP projects like Content Management Systems go through huge social upheavals and fork into seperate projects on a regular basis.
For example, take this one
http://next.ohloh.net/projects/14
NOBODY writes 1.4 million lines of PHP on their own in one year.
Either your PHP "lines of code" scanner is whacked and can't handle projects like that (i.e. it is including HTML or something) or you are essentially massively amplifying the line count as large PHP projects fork.
Joomla! is a nother example. Millions of "lines of code" in one year? It's just not possible unless you are forking other projects outright.