The Hub

I'm restoring an old parlor guitar. I have just discovered that it plays 20 cents sharp. Thats not in and of itself a mystery, usually. This guitar however has exactly the same distance from the nut to the 12th fret, and from the 12th fret to the "saddle" which is now a small shim under the two E strings both are 12 3/32"...with room in front of the bridge pins to finesse the location of the saddle slot, which I have not routed yet) I set the bridge position to achieve this. To be blunt, what the hell is going on?? The string action is just under 3/32" at the 12th fret, and comfortable at the nut. 20 cents sharp?? I'm baffled. This is WAY beyond "give or take" it's off the charts. Is the ghost of Pythagorus pissed or something?