Okay, I have a Fender 90 watt SS combo amp and a Fender Fat Strat. Every time I do a downstroke (starting on the 6th string), I always get this loud ass thumping sound from that 6th string. No matter what settings I try, I always get that LOUD freaking thump and it's so annoying.

Is this just a problem with Fender amps? Is it my guitar? Does aybody else have this problem?
check pickup height, lower the bass end...could be your playing...also try a compressor
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