I seem to have figured out my problem. Not exactly sure what they did, but when Go Launcher installed, the dock shortcuts are set differently.
I first encountered the issue when using their default dock "Contacts" button would make my phone forget my "Contacts to display" option, showing ALL my contacts every time I went into it. After about two weeks I used the App Drawer shortcut and like magic, the setting stuck. I deleted the dock icon and reset it with the app drawer one.
I just tried the same thing with the Phone button. Using the default dock icon always takes me to the Dialer (and happens to be the icon's default name). Using the App Drawer's "Phone" one takes me to the last page used so I put that on the dock instead.
If you guys are using launchers with dock shortcuts (specifically one named Dialer), try using your app drawer/Phone shortcut and see what results you get.