Try installing your updates manually
Updates start here and select product, read to see if you need to install updates in number order, or if the updates are cumulative for the individual product http://www.adobe.com/downloads/updates/
Also, CS6 is 3+ years old and will not be updated for new operating systems or hardware... so if you have a high definition display, this are likely not going to look right
Thank you; I found this link right before you replied and didn't delete the question right away. Prelude and Speedgrade now appear normal. Others such as Dreamweaver and Audition, but luckily for me these aren't as necessary. The main ones I need are Photoshop, Speedgrade, Illustrator, Premiere Pro, and After Effects and luckily these all look normal now with the updates.
Do you happen to know the issue with the Flash Builder not installing?