Start with a coarse mesh. Decrease the mesh size in steps and observe if fluctuations are taking place again. It can give you some direction as to what is happening with the software.
What is your turbulence model ? Also the mesh can caused a problem. Algorithm correction ( interaction between speed and pressure).....
I worked in 3D with solar heater and I used boussinesq approach for turbulence model. Another think your boundary layers use the conditions mass flow in the both input and output.