Sound fades after 15-20 minutes

Please illuminate me explaining the word "Muffled" means and i will be glad to help you out...

Sounds like a resister is bad..

Sounds like bad power supply capacitors

The Efx 12 has two outputs monitor out as well as mix out ( XLR sockets ). If the level bars are moving its an indication that the mixer is working. Have you tried headphones out as well as monitor out.
What is your amplifier and speaker setup- you have not mentioned it at all.
Even if any PFL switch is on you won't get sound out of the speakers.
PFL stands for Post Fade Listen and when any of the 12 channel PFL switch is on only the headphone out put will work.

Clean all back switches, including the Stereo/Bridge one with a cleaning solution spray, then check functionality again.

Brand new? Take it for warranty repair IMMEDIATELY... don't mess with it !!!

The only thing for you to check is that you did not turn on "STANDBY" as this shuts down the power amp and the capacitors will bleed off and sound will fade. Try switch in both states before complaining

ONLY use the amp in STANDBY for a brief period (20 seconds) to let the tubes warm up... Leaving in STANDBY for a long period straains the input filter capacitor. If you are done with using the amp, turn it off...

Make sure the STANDBY switch is not pressed. It will fade sound out on the first 8 channels and keep it off.

Looks like capacitor problem.Check power supply section also.

First check if you get sound from the headphone jack.

Do you hear anything as the power comes on from the speakers..? A slight bump?

A lot of these dead audio things can be traced to a failure at the expression pedal. often these use a light dependent resistor and the illuminating lamp burns out. This is all down by the pedal.

Many of the Yamaha organs, including the FX20 I have, have circuitry that checks that the power amp has DC balance before a relay closes to connect the speaker. A failure in the amp can cause dead sound as well.

have you got valves fitted to the amp as they can cause fading if old >damaged >not fittted properly also check the speaker connects and try playing half volume the output should be steady.. you say its handmade if you made it pull out the amp board and check your soldering joints look to see fi there is any that need resoldering as they may be getting hot and causing a resistor to fade..