MB Quart is a Maxxsonics amp... you can find the same build Hifonics used in their amps. i take it that it is a FX1700 ? being a Maxxsonics board, i would not assume that it is good, even if it is brand new... you get what you pay for, and i have worked on literally thousands of them. including the boards used by Digital Designs, American Bass, Audioque, DC Audio, etc, etc. they are all made by the same manufacturer in Korea and China. the bigger amps being Korea, and most of the smaller amps like the MBQ being China. i have seen them not work brand new out of the box.
you did not explain how you determined the amp was good... did you hook it up in another vehicle ?
know that if you do have the FX1700, it is a 2 ohm minimum stable amp. measure your speaker wires and make sure you have more than 2 ohm load. while that amp can run a little bit lower, it will live an extremely short life.
yes, you can blow out the RCA outputs for the sub on your head unit. people do it all the time by hot swapping the RCA's... in other words, not turning the unit off before unplugging and plugging the RCA's. if your head unit has 3 pairs of RCA outputs, then there are 6 surface mount transistors driving them. 2 of them for the sub. your mistake is you were measuring DC... if you see DC on them, then that means one or more of those transistors are shorted. you should be measuring AC. you should see the AC voltage go up as you increase the volume.
try something... hook everything up except the RCA's, and then use an ipod or MP3 player, phone or whatever with an headphone to RCA adapter, and plug it into the RCA's of the amp. if the amp is really working, then it should play. if it does, then swap the RCA cables. should work, unless your RCA output from the head unit is bad.
if it does not play, then the only thing it can be is the amp. ( since you said the speaker is tested good )
but before you do anything, make sure that your RCA's are plugged into the input RCA's of the amp... not the output RCA's. seen that many times...