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#11
It's somewhat unusual that there's no System flag on Recovery showing that the boot files do in fact reside there. However it's not enough to move Active flag if you didn't move it there yourself.
But just to be sure I'd boot into Win7 DVD or System Repair Disk to run Startup Repair - Run up to 3 Separate Times to see if it finds some things to fix and plants the System flag on the Active partition where it should be. This may help with some of the boot-related issues.