Pads or Keys....why does it sound different???

Well, "terrible" probably means "not the way I want it to sound", as opposed to some objective measure of "wrongness".

Even so ... let's break this down. The Fantom does not do what you WANT it to do, it does what you TELL it to do, or at least what it is SET to do. That's a key concept that many seem have trouble understanding.

Sooooo, if it sounds "wrong" to you when you assign a sample to the keys as opposed to the pads, you need to ask yourself "what's different about how I have the keys setup than how I have the pads setup?"

Most likely, it's a matter of having effects applied differently to the keys than the pads.

Yeah it probably does have something to do with the effects on the keyboard in fact thats exactly what it is. Now I need to find out how to shut it off and have everything level.

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Don't forget when using the keys the velocity isn't set to a specific like the pads are. I think the pads are set between 100-127 by default, the keys are how hard you press them (assuming that you are playin the sample with the middle C key).