Capacitors in general have wide tolerance, the lowest capacitance in the string will hit zero first, and may be back-charged by others that held more charge.That does not sound possible (to me). The thing that seems most relevant is that voltage in a capacitor bank is a dependent variable - charge is the determining factor.
The charge on each negative plate equals the charge on each adjacent positive plate. For the charge on one to be reversed, they would all have to be reversed...right?
When you say that you have done this with smaller capacitors, do you mean you have set up a series bank, charged it up, then rapidly discharged it - and some of the capacitors have ended up with negative charge while others are positive?
I think this could only happen if you put in some wacky extra circuitry to make it happen.
This often happens with Ni-Mh & Ni-Cd batteries - a weak cell will be repeatedly reverse charged by the others - they don't last long when that happens!