I've read this thread carefully, and although I'm no sort of expert here, I
think that only Meindert is getting at the truth. Most of the rest of you
are getting confused between voltage and current. Because both batteries are
connected in series, IRRESPECTIVE of the charging mechanism (eg alternator
or smart charger), then both receive an identical charge. If charging starts
from a state where one battery is more discharged than the other, then the
fuller battery will replenish its charge before the other one, and towards
the end of that charging regime its terminal voltage will rise fairly
suddenly from around 13V to around 14.5. Now, depending on the precise
characteristics of the charging source (different for smart chargers and
alternators), the ONLY way that the undercharged battery can continue to
receive charge is to overcharge the now fully charged one. This implies
applying more than 14.5 volts across the full battery, and this will, of
necessity, cause to battery to gas, perhaps even boil in extreme
circumstances. Enough said?

Guy is probably right in saying that small additional current drain from one
of the two batteries is lost in the noise, as it were. But as a concept,
asymmetric current from series-connected batteries is bad news.

Interestingly, one could get round the problem described above by putting a
14.5V zenner diode around the battery which is not being drained by your 12V
circuit, but this isn't without problems either - the diode would have to
be capable of handling the maximum charge current, lets say 30 amps. 30A x
14.5V = 420watts - thats a pretty big zenner on a pretty big heatsink!!!!
HTH