Recorded parts don't line up properly

good luck
ive had this problem forever and have had no help

Not sure if it's related, but FWIW, there are a couple different looping options in Sonar.  You can have them both going at the same time.  Make sure you have them set correctly.  There are the regular loop points that you can set, at the beginning and end to have Sonar loop a particular section of music, then there are the Record Punch In And Punch Out Loop Points, which can be set separately.  These actually tell Sonar where to start and end recording.
 
https://www.cakewalk.com/Documentation?product=SONAR%20X3&language=3&help=Recording.26.html
 
Hasn't happened recently, but I used to have a similar problem where the last recorded track would shift, after I recorded it.  I could see the waveform start drawing at the correct point during recording, but as soon as I stopped the recording, the track would shift over a measure or so, putting the track out of sync with the rest of the song. Drove me crazy.  Never did find a fix.  My guess was that it had to do with a rogue vst plugin which was causing timing problems.  If I closed everything down and restarted my computer, it would fix the problem.