After you're captured by lockhart and the ceph attack, when you wake up, you still have all of your weapons... But after you wake up in the start of "Seat Of Power" not only do I still have all of my grenades, C4's and JAW's, but I am now carrying 3 weapons! (SCAR, Marshall, and DSG-1)
I think that this is a bug that Crytek need to fix.