Maybe the hookup into the amp is bad? I have an aftermarket head unit in mine and had a buddy install it for me. The harness I got off amazon didn't work correctly. Luckily he had one that did and I returned mine. I have the JBL as well and I ordered the correct stuff, the "convertor adapter box thing" (to be super technical) that hooks into the jbl amp just was a dud for some reason.
Also, if that's not it, if for some strange reason the previous owner had the audio settings messed up on the stock HU and swapped the aftermarket in without zeroing everything out, I know that causes problems. The amp retains whatever settings where last put into it from the stock head unit. For instance, if you had your balance all the way to the right side and the bass all the way up and the volume at 5 when you removed your stock head unit, the new head unit will go in and treat those settings as its base. So the new head unit wouldnt be able to exceed volume 5, and the base and balance would stay the same. That's why the instructions say to turn the volume up and zero out all of the settings before taking your old HU out. PO could have screwed something up there.