How? It seems exactly the same thing to me.It doesn't surprise me that this would be the case - the role that a below lens contrast filter plays in an enlarger's light path is very different than the role that a camera filter screwed on to the front of a lens plays.
The only change I think that below-the-lens filters cause is slightly increased flare. Since you are adusting the contrast anyway, I don't think it matters. I was too cheap to buy the nice plastic Ilford below-lens filters so I bought the 3" above-lens filters and I use them below the lens. It works.