When you Time Profile a single application, a "sample" is whenever we see your application doing something. So, 1000 times a seconds we check to see what is running on the CPU(s). If a CPU is idle, nothing is recorded. If a CPU is running another application, nothing is recorded. Only if your application is on a CPU at that instant do we take a sample and record its backtrace.
So yeah, 35% of the time when Instruments looked and saw your application running, your app was in that particular block.