So, I don't know if this will help anyone figure out the problem, but I wasn't using WPTouch and I was having the same problem... and not just on mobile sites. Deactivating EVERY plugin helped - for awhile. I eventually got it up to Jetpack and one other plugin, but then the problem started up again. I deactivated everything, and it went away... save for IE (version 9 is what I had to test with).
As far as I can tell, the problem just comes and goes as it pleases.
BTW, the kicker is that I have a mock site I was doing some testing on - source code is identical according to http://validator.w3.org - and THAT works w/o any problem. I think it might be a WordPress problem. The mockup site isn't running 3.8 yet, but another one (also working) is. The other one is lounge.findstuff2read.com
I'm going to hunt around the forums to see if somebody else had a more similar situation to mine, but if anyone here can help, I'd appreciate it!
My site is http://www.FindStuff2Read.com. My mock-up site is http://www.FindStuff2Read.com/3.