Well I just realized I was an idiot.
Earlier the CTRL/ALt combo didnt work anymore, it started doing CTRL+ALT+SHIFT again. Then I clicked on the F (frame) button right next to it and it was also CTRL+ALT+SHIFT. It drove me nuttttts. Then I noticed it was on the same horizontal row and tried different buttons on that same row and it was doing the same thing. I decided to turn off Radial Menu and it fixed the problem.... Eventhough I had radial menu minimized when I was working with TabletPro, it was selecting unwanted buttons on certain rows. So my problem was having 2 touch programs up at the same time.
Tomorrow I want to play with swiping to see how I can change profiles, that way I can make another set of buttons dedicated to my other softwares. I use them all differently.