That sounds like one box or one driver in a box is out of phase (wired the wrong way round). Check through the system to see if its all wired the right way around. It could also be one of the cables going to the cab so check this as well. Connecting a battery to the wires that go to the back of the amp should make all the drivers pop out in one direction.

+1 sounds like out of phase had this problem before running one scoop had thunder linked a second killed the thunder half an hour before dance was gonna start sorted it just in time

But if some speakers are old and some new can that be an issue when the ports are so close to eachother?

There may be some very very small difference in compliance of suspensions between old and new, and and old driver may have some partial thermal damage of its voice coil, from the event that killed the other drivers, but from what your describing, it is a phase problem, i.e. one cone/cabinet is moving forwards on a +ve signal, and the other is moving backwards, relative to the audience.

Don't take it as read that applying +ve to the +ve terminal will push the cone out.

I have mentioned it before but to remind people...I had an Ohm MR228 (2 x 8in side by side drivers) that had been reconed and couldn't reproduce any low frequencies; one of the drivers pulled the cone in with +ve on the + terminal. The reconer had wound one coil the opposite way.

No..first thing I checked.