FYI for everyone, especially Mr. Laser Beam. I called Sony customer support and they walked me through shutting down the "upscaling" on the blu-ray player. Although it isn't as simple as turning it off, my blu-ray player has the option of turning on and off the BD-DVD- ROM 1080p format in the screen options in the main menu. Once I turned it off, everything went back to normal.
I asked what that did, and the man on the phone said that it essentially turned off the "upscaling" the blu-ray player does when a dvd is inserted.
I can't tell the difference in quality as I actually believe the DS9 conversion to DVD sucks anyways, so it makes little to no difference. It still fits the screen and isn't pixelated.