Batteries connected is series have to be the same type and same state of charge. Virtually all batteries are cells wired in series but they were the same when it was new and theoretically they stay relatively the same. When one cell gets weak, the battery is toast. You are just seeing that effect with separate batteries.
There are troubling problems with batteries in parallel too although GM tried it with some of the Diesel cars. You pretty much had to replace them in matched pairs too.

Greg Fretwell