Hmmmm...... well I don't know what to say then without hearing it originally. You could have had a defective sub or possibly a refurbished one if you bought it from a unauthorized dealer.

 

Ok so my replacement sub finally arrived. I want to insure that this one wont blow. If I have the crossover set at 100-110 ish and the gain at halfway and the bass eq set at 1/4 I should be okay correct?

If you will remember, I have the Alpine MRP M-500 and the JL W3V3-2.

 

set cross over to 80 hz.
do you have an aftermarket deck? if you do set it to flat - or 0 for the sub and set that cross over to 80hz as well

play 3 -5 songs you know really well and go from the drivers seat to the amp increasing the gain until you're happy with the amount of bass you have.

leave the bass eq alone

 

Its the stock bose system. So I should turn off bass eq entirely? How far should the gain be set?

 

gain is something that should be set by ear. if you notice the sub pushing passed a certain point or it's making an odd sound STOP and go back 1/8th turn. that is the sub's maximum point. to do this properly listen to songs you know very well. if you hear abnormalities with the bass turn it down.
As for bass EQ I just avoid it because most of the time it doesn't do much for the average consumer. If you had a complex bandpass box. it would make a difference