I have found what I believe to be the culprit, iNotes adds a meta-tag to emulate IE9.
<META http-equiv="X-UA-Compatible" content="IE=EmulateIE9" />
Lothar Mueller pointed me in the right direction.
Domino 9.0.1 Fix Pack 5 adds a Forms9s.nsf which allows you to get rid of "Quirks Mode" for IE backwards compatibility. After installing the FP, the new forms9s.nsf file is installed, then you update the notes.ini with
and it eliminates the emulation tag for IE. I still have to test my iNotes customization apps, but this gives an option for running some IE features that didn't work before such as Ajax requests from iNotesExt_9.nsf, etc.