The software can only 'see' what Windows reports to it. Switching from the Presonus to the onboard sound card won't make a difference unless you change what the input is in Preferences, and you might need to change the Driver Mode, too.
Do this: Go to 'Options>Audio', or press the P key on your computer keyboard.
What is listed as the Recording Timing Master and Playback Timing Master? What is the Driver Mode? (Sometime around the release of MC 6 or 7, they changed the menus from Options>Audio to Preferences using the P key. I don't know which menu your software uses, having neither 6 or 7.)