Seems that subwoofers are a wild cat of sorts. We build monster capable subs and taming them and getting them to behave is the tough part.
I know phase is an issue, but what if your DIY design has no phase adjustment.
Frequency response at the cross over point is a key issue and matching SPL of the mains and center.
Time domain issues. Is it just a delay error for you ?
On any plate amp you will find a phase adjustment.On most all processors you will find a delay settings page.Do these two coincide with one another ?