Thank you for your post.
I am unable to replicate this issue using Internet Explorer 11.0.7 under both Windows 7 and Windows 8.1. In my test, I was accessing the FMServer_Sample.fmp12 file.
Does this shifting only occur with this one file? Does it occur with the sample file?
Any other information you can provide about your computing environment may be helpful in determining possible causes.
I have only tried it with this one application. I've attached the screen shot for the same screen in Chrome.