Changing velocity on midi changes the time of the note.

I guess you're using an older version of SONAR because right-click in the PRV has been Delete rather than Properties since X1 - unless maybe you're using the Select tool instead of the Smart tool...?  In any case, I'm not sure how that would be happening when changing velocity in Properties, but I recommend you start changing velocity by dragging the velocity hotspot on the note instead; it's much faster if not quite as precise. Better not to get too hung up on hitting exact numbers, and just use your ears. With Velocity Audition enabled in Editing preferences, you will hear the change as you drag the hotspot.

Thanks for the advices:)
I found out this issue happens just on really heavy and long projects not on the others. It must be a bug or something like this. I always use smart tools and select tools and haven't had this issue before . I see this problem just on two projects which they are so long about 45 minutes and full of plugins. but on the other projects it is fine and doesn't move the midi notes.