Odd issue in latest update in sonar X3 professional

Maybe it's something that I'm doing, but I think I am doing what I always do since I started using cakewalk and I never had this happen before.
 
I compose my music at the piano and then I come to sonar and enter my song using the staff view. I select a quarter note and then set the snap to the same. I enter the notes of the song, changing the values as needed. When I then play it back, it sounds odd...like some of the notes are being clipped or are being played staccato. But they were entered all the same way. (I did try using the click on the last note used method as a way of speeding it up. At first I thought that was maybe causing this issue because I hadn't used that method before and choosing the last note used does not update the snap value, but when I went back to my old method, I still got the same issue.)
 
Also, I had four eight notes in a roll...all entered the same. But one of them played shorter than the others. I right clicked on each of them and checked the properties and one of them had values in the fret field that the others did not have, but I was not able to change it to match the others.
 
I even tried dumping my file and rebooting. I even switched between rapture pro and Dimension Pro. Same results.
 
Then I switched to the piano roll. I noticed that one of the problem notes was too short. I thought "There's the problem", but I didn't see how that happened. I used the snap to option and Fill Duration and the other one I can't think of were NOT checked. I went to stretch the note to the proper length and I saw it was the right length, but it was overlapping the preceding note. (But everything looked correct in the Staff view!) And then I noticed there were other notes overlapping the preceding notes as well. In the piano roll it wasn't always so obvious, as the notes were other on different keys, but you could check with the NOW time indicator. Once I fixed all the slight OFF timing values, the music played as I had written it.
 
I went back and checked the Staff view. I expected it to be messed up now, but it was still corrected. 
 
I have tried this three days in a row now with new projects and updating my current project and I always get the same effect. I have to go to the piano roll to fix the timing issue. That's OK as I'm starting to prefer the piano roll view over the Staff view. But is this a bug or is it something I'm doing?