hmmm thats odd. does the beep come from the speakers or the HU?

What i would do, take out the Head unit, and disconnected the speaker leads from the radi harness to the adapter harness.

then take a 9 volt battery and touch +/- to the +/- on the leads that shoul dbe running to the speakers, NOT the ones on the aftermarket radio harness. See if the speaker makes a little popping sound.

if it does, then the wires are fine from that point on.. could be a setting in the HU or the amp is shot.. what HU?