I have some epub files. And it is usually use media-overlay.
Before I updated chrome browser, there are no problem.
After update chrome browser to 46.0.2490.71(new version : Oct. 13th 2015), media-overlay does not synchronize properly.
I tested old version of chrome browser(45.0.2454.101). it is OK.
I tested follow browsers.
Chrome browser(Mac : 45.0.2454.101) : OK.
Chrome browser(Windows, Mac : 46.0.2490.71) : Fail
Safari(Mac : Readium-JS-viewer) : OK
iBooks : OK
I don't know the problem causes chrome or readium. Please, check this problem.
https://drive.google.com/file/d/0B9vxuQhnhF6rZ1BBcWk3RG82aUU/view
Thanks for reporting this. I have directed this to our media-overlay expert, who should respond soon.