I couldn't figure out how to reset all my preferences through BitComet but instead I cut the original corrupted bitcomet.xml file and put it on my desktop and then started up BitComet. The User Interface was normal and I proceeded to input my settings from before. Everything seemed normal after I exited and started the program up after putting in all my settings except for one thing, the main window wasn't supposed to appear, it should have been started up in the system tray. After noticing that I was staring at the main window of BitComet instead of my desktop, I went into the options and realized that I forgot to change the default option for the appearance -> Main Window Placement from "Show Main Window" to "Minimize to system tray". I quickly changed the setting and exited the program. I started it up again just to make sure everything was ok, but it wasn't. The program did minimize to the tray but when I went to go check the main screen of the program the User Interface was screwed up again. I went back into the options and under the appearance tab I changed it back to "Show Main Window" and applied the setting. I exited the program and started it up again, and the User Interface was perfectly fine. I then again changed the setting back to "Minimize to system tray", exited and restarted the program, and again saw that the User Interface was screwed up again.
I don't know why this option is causing the User Interface to get screwed up. I haven't checked each and every option one by one yet, but I'm fairly certain that this is the culprit.
Also, I'm not sure if this behavior is intentional but in BitComet 1.29 when the program starts up, it immediately would scroll down to the bottom of the task list so I would be looking at my latest tasks. In BitComet 1.35 it shows the very beginning of the task list after it starts up.