new cell, batts arnt as punchy

Hey i recently bought integy 3600 7 cells and man they were beast on there first couple of charges. I was flipping in 2nd gear. But after a jump one pack flew out and scraped up a cell so i had to replace it. Once i replaced that cell it seems that the batts arnt producing the same torque as before. Is there something i did that altered this? Also my motors shifted on the mount and i am unaware of how tight the meshing should be? SHould i put them as close together on the spur gear as i can, or is a loose fit better? thanks.