I'm having issues searching through PDF documents that I print into OneNote 2013 (from any source - Adobe Reader, MS Reader, etc) when the system scaling is not at 100%. It seems that if a document is printed into OneNote when the system is scaled to some higher value (say 150%, which is common for tablets), the search locations will all be offset and not in the correct places.
If this import/print is done with the system at 100% scaling, then the search works correctly. If the OCR is redone (Make Text Searchable -> Disable, followed by do it in English), it will work correctly but only if the system is at 100% DPI scaling when the OCR was performed. Any time it does OCR at a non 100% scaling, the search will not work properly in OneNote. I've tested this on two computers so far so I'm beginning to think it's a bug in OneNote or something closely related to it.
This album demonstrates the issue: http://imgur.com/a/fMSUP
Does anyone else have this issue? My current (very annoying, especially on a tablet like the Surface Pro) workaround is to use 100% DPI scaling in the control panel when I do OCR for a document. It's very easy to test if this issue exists on your system as well - just change the text scaling in the control panel, print any PDF with text to OneNote, and then try to search that PDF inside of OneNote and it will highlight incorrect locations.
I imagine the issue is similar to this, but that was apparently fixed for the 2010 edition.