This behavior greatly depends on the counter used. If you are using the User or User+Kernel Time counter, AQtime only counts the time spent by CPU to execute your code. The time spent to execute code of other processes or threads is not counted unlike when using manual timers.
The Elapsed Time counter should demonstrate results similar to those you get, but even in this case there can be some differences caused by overhead added by your timer handling code.
You can find more information on different counters' specifics in the Counters Overview topic of the AQtime help system.