While the boundary conditions remain the same, the GPU solver might not have included the all the solver settings. Please see this section of the user's guide: 34.9. Features Supported by the Fluent GPU Solver (ansys.com)
In the Fluent console, do you see any messages regarding a solver settings or any value being changed because the GPU solver is enabled? This message usually comes up before the iterations begin.
Also, I would compare the Fluent transcript file of both the CPU and GPU runs to check if there were any discrepencies.