Can you check the NWBC_CFG (or the UI2 one), does it have FORCE_BROWSER_STANDARD_MODE set? See SAP note 1898981 for details. I'm thinking there must be a conflict meaning one level is setting standards mode whereas another one isn't. You need to use transaction /UI2/NWBC in order to launch NWBC for HTML 3.6 which defaults to standards mode.
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