I have seen that the N900's file management can turn tricky/ faulty. It was after using the newest version of PC Suite for copying photo's. I could not find photo's outside the hidden .pictures map. But any map I saw twice now!! In USB usimg my PC, I copied all of my copied photos (placed in the root) to .pictures/my pictures (new map) and they showed up. The double maps were gone. I've had mostly no problems since. usimg an older 1.39.3 version of pc suite. That version synced well to. Sometimhes the pictures app still does not show them all!
Work around: 'diashow' them first, them I see them all... Maybe you could check the place of the files?