was your application adressed to the UKCAA?, I passed all my modules in feb 2010 and started my logbook as of 2008 and still had my application accepted.
And I got my B2 license 5 months ago.
Another mate of mine got his B1 a few weeks ago and he just a few months ago passed all his modules, and still didn't have a problem.
Experience is experience and it doesn't matter when you gained it.
There must be something odd about it, If it's been adressed to the UKCAA you may have to phone call them for further enquiries.
Note: back in time before I apply for my license there was a rumor making the rounds regarding what you had said that the application may get denied if you passed your modules whilst you're on your 2 years experience stage however my application went straight through and
I had no problem, I'm quite astonished that it did happen to you.