Don't forget browser.js (also in the includes folder). Here are some updated build files and an updated browser.js file I have lying around here. Hopefully they'll take care of things for you:
Keep a backup of the old ones, and replace them with the files in the attached archive. Keep the original blank.gif and REMINDER.txt files as they haven't changes and are not included in the attached archive.
BTW, the menu won't show up at all in IE 9 without these newer files.
The browser cache may need to be cleared and/or the page refreshed to see changes.
If you want more help, please post a link to the page on your site that contains the problematic code so we can check it out.
Oh, and if you have a horizontal menu, add this to the head of the page:
<!--[if IE 8]>