Problem after clean install Sonar X1 Pro

Since I did a clean reinstall when I record a new audio track, it's not sync'd with the previous recorded tracks -- it lags several clicks. I can manually shift it over to correct it, but it's a pain, and it never used to do this. This is with all clean audio tracks on the project, no plug ins or effects.
 
Any solutions?
 
Also, most of my Cakewalk process audio effects are missing now.

Your going to want to list some specs first. Like:
1- your soundcard
2- Which version of X1
3- Windows OS
 
To me it sounds like a latency problem but without enough details im blind really.