The problem was, whenever I launched these games the tracked bat would be 90 degrees off on orientation, this was obviously an issue as if you were holding the bat up straight with the handle pointing towards the floor it would look like the bat was horizontal in front of you.
I searched for an answer for this and had trouble finding a fix, after a while messing around I found out there were settings for the trackers but not outside the headset in the windows SteamVR app where things are normally stored but inside of the SteamVR menu once you have the headset on. After altering these and setting the tracker to be on my waist rather than in my hand it fixed my issue, if you have found this post and have this issue I shot a quick video of how you change this and what fixed it for me.
