I'm comparing two different methods for solving the Navier Stokes equations. Why are my velocity results so different?

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I want to use a code for modeling 2-D fluid flow out of a tank to understand a chemical process. The code has never been used for pressure boundary conditions, so I want to check that it works as it should. I'm doing this by comparing results with those from another code.

The comparison matches very well when I use a velocity boundary condition at the bottom of the tank. However, there is a large discrepancy when I use a pressure boundary condition. In both cases, the outlet pressure is zero. My problem is that I need to use a pressure inlet condition, not a velocity inlet condition. I have active questions about this at the engineering part of Stack Exchange. However, I have been stuck for a few months now. It occurred to me that it might be a mathematical problem.

One of the codes uses a Galerkin finite element "perturbation method" (penalty formulation). So it eliminates pressure from the Navier Stokes equations. The other code uses a "volume of fluid" (and finite volume) method that does not eliminate pressure. I have tracked down the person who wrote one of the codes and people experienced in using the other. They have checked my setups and cannot find anything wrong.

I'm not a mathematician and I'm also not that experienced with fluid dynamics, so it could be I'm missing something simple about why these methods lead to such different results for pressure boundary conditions. If anyone familiar with the methods could offer any advice, I would be very grateful.