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.

Track sync is handled by your audio interfaces driver. 
Make sure you have preferences set to use ASIO and Sonar should look after this. 
If you are for some reason not using ASIO driver then you will have to do a loopback test, determine the latency and use the manual offset to try and fix it. 

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.

Thanks, everyone! Got it fixed! Now, if I could only find my missing Cakewalk effects. For example, the FX compressor/gate...