Intonation is affected by more than the string length, though that is the main factor. Sounds like you need some adjustments to the nut. If the nut slots are not low enough, you pushing down on the string to fret the note makes the note go sharp, as it would if you were bending the note. Not anything huge. A reputable repair person should be able to take care of it pretty easily. It will also make the guitar play better, so don't hesitate to have it done.
