Wow, you have quite the discrepancy compared to me. I know part of the difference between GC.com and Project-GC numbers is that PGC doesn't count pictures from TB logs, and possibly even 'write log' logs. I'm not 100% sure about the 'write notes' though.
Anyways, I've had the same theory (logs with pictures, not the number of pictures in logs) as well but the math still doesn't work for me. In the first 2 pages of my gallery, I already see that I have at least 5 logs that have multiple pictures (2 or more) attached to them so the numbers in PGC would be further out of sync if that's the cause.
So as far as I can tell, it remains an unsolved mystery for now....At least I know I'm not just me now so thanks for replying. :-)