Well disconnect the amplifier and see if the parasitic drain improves, thus you'll know if its the problem or not.
A couple of questions on the AMP?
Is it OEM or aftermarket Amp?
How is it wired? Straight to the battery with the blue lead from the stereo to turn it on/off?
Have you checked your battery voltages? Have you checked your Ignition Off Draw with a multi-meter to see what it actually is?
Personally, I thought I had the same problem in my Commander (Aftermarket Stereo but no AMP), it really turned out to be I got two battery's in a row bad from Walmart. At least in my experience, the Walmart Battery in the Commander's size is just inferior quality, both of them went bad within 6 months. I've had other Walmart Battery's in the more common sizes and never had a problem, so it may just be the uncommon size for the Commander that is a problem for Walmart's Brand. And both of them would operate just fine, unless I left the car off for more than 24 Hours, then the battery would go dead.
Instead of going for a 3rd Walmart Battery under warranty, I just went and got a different brand, and sure enough, no more problems, been two years and the battery still going strong and not going dead.
But the proper troubleshooting would be to get a multi-meter and set it up to measure current and put the leads in series between the positive battery post and positive battery cable. Read the amp draw.
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