Yes, header uses the HTML5 and CSS3 flexbox, regretfully IE has partially support FlexBox Layout. See the Known issues tab on that link and see if you can apply the fix on your configuration. If you want to fully support the IE browser, since you have a basic header layout, I suggest that you use the standard header instead.
Regarding the background video, IE does not support the .webm format, please upload a .mp4 format and add it to the background video URL field separated with vertical bar
Hope this shed some lights,