Many things can create this situation but to at least get you going:
Check the polarity (+ and -) on all your wiring from the head unit all the way back to the speakers.
On your head unit, what kind of equalization capability do you have -- where is it set?
Maybe you only have simple bass/treble control, what happens when you adjust?
You mention your speakers are 250w RMS -- at what ohm (resistance) rating?
You mention your amp is 100x2 peak -- what is its RMS rating and at what ohms?
(As you have already touched on, gross mismatch between what the speakers need/are pulling versus what the amp can deliver and at what resistance is a good possibility based on your description...example, your speakers are rated at 2 ohms and your amp isn't even rated to go down to 2 ohms but needs a load of 4 ohms or more...)
Are the power and ground wires to your amp adequate for the needed current. (Did you use the gauge wire recommended?)
How are your speakers mounted -- or are they yet?
Do you know for sure each component is working properly -- how do you know?
Lots of other things regarding low/high pass filters, crossovers, gain controls etc. but perhaps check the basics out first....
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