UPDATE:
I fixed it! Not sure exactly what caused the problem, or if there was really a technical way to fix it, but all I did was delete a bunch of my tweets. I used an app to delete at least 3,000 of my tweets, and once those 3,000 were deleted my new tweets started showing up. I understand that this may be a bit of a drastic measure but I didn’t know what else to do, Twitter Support couldn’t help me.
This is the only way I know how to fix it, if you don’t want to delete any of your tweets then I’m sorry I don’t know how to help you. 
Here is the website if you’d like to give it a try: http://www.tweetdelete.net/index.php
its 100% reliable and you can turn it off at any time. Hope this helps.