Factory amp was probably not bypassed (as it should be when upgrading to an aftermarket deck). This could be the cause of poor performance. Or, some of the speakers might be wired out of phase.
1999 Ford Contour SVT #900/2760 (SOLD)
2005 Mazda 6s
2003.5 Mazdaspeed Protege
1998 Ford Ranger 4x4