I'm not in the least surprised -- scripted shims are fragile enough; trying to run TWO of them at the same time; that's just begging for it to blow up in your face. Tossing jquery nonsense on top of that and you've likely so completely over-thought your page you'll be lucky if the traffic isn't 100% bounce and it crashes even modern browsers.
To me it sounds like you are ice-skating uphill with technologies not ready for use on production websites. Likely not your fault with all the idiotic bad advice out there about HTML 5 that seems to exist for the sole purpose of nube predation; selling new books and seats at lectures, instead of promoting good coding habits, practical and easy to maintain methodologies, and doing what the web is actually for -- delivering content to users.
That said, your snippets are gibberish without seeing what it is all that scripting is being applied TO. The shivs could be getting confused by invalid markup -- whatever it is you're loading the jquery for could be latching onto the window events impropery or conflicting -- Without actually seeing the page in question, anything we tell you is a wild guess based on no real facts.