Hello,
Normally the tracer value, when you use this option for fluxes, must be between the previous value and the precribed value. Second thing, it is true that both options should coincide when you refine the mesh, but this must be done with changes of the time step also, and after some refinement truncation errors may complicate the process.
Now does everybody has the same problem? Think of a very very large element near the boundary, going deep into the interior of the mesh, with an arbitrary small time step, the latter so that the flux should be arbitrary small. Then if you impose a prescribed value, the quantity you add in the mesh (through linear interpolartion over the large element) will correspond to an exagerated or even infinite flux. Everybody has this problem, but you realise it only when you carefully check (and print) the conservation of mass in the form : final mass = initial mass + fluxes.
With best ergards,
Jean-Michel Hervouet