I realize this is a late response, but yes, I have noticed "cancels" coming in at different times with certain operations are performed.
Not sure if you were able to make any headway in investigating this as to why you are seeing cancels popup, but here are some of the reasons why I (believe) they occurred in my case:
The Project Server administrator actually “cancelled” the queue job from the Manage Queue page.
Project Server found redundant jobs in the queue applied its internal “optimization” algorithm that will cancel the redundant job so it does not waste time and moves directly to the job it determines is necessary to preserve data integrity.
For example, if you save three times, Project Queue will process each of these 3 saves b/c it does an “incremental” save and must allow each one to complete before any other jobs for that particular project file are processed.
Now, if a save if done followed by a publish, and then another save is done, followed by another publish, the Project Queue “optimizes” this situation based on its internal data integrity engine and will process the first save, cancel the first publish, process the second save, and then process the second publish.
The last situation I can think of is if you are experiencing cancels on your check-in jobs. This from what I’ve seen usually points to a SQL Server contention and may be resolved by increasing the SQL Retry interval in the Project Server Queue Settings page.