For non-gel type (now old fashioned) batteries, that you can remove the vent plugs, I've found that a valuable addition to the tool kit is a cheap hydrometer (pay no more than 3 or 4 quid!). Has saved me hours of red herring time over the years!
Suck up the electrolyte and measure the relative density (used to be called SG or specific gravity!!). Each of the six cells should go flat together and charge together at pretty much the same rate (charged is around 1270 but the cheaper hydrometers show a simple green/red for charged/flat). If a cell has "gone down", it will be all to obvious (as you saw by noticing that one cell wasn't bubbling!).
Also another tip for battery maintenance, is NOT to jump a flat battery (if it wasn't damaged in the first place then it might be after a jump!) and to only use "intelligent" trickle chargers, NOT high charging car battery chargers. The early advice of an Optimate is good, also Acumen Platinum/Titanium/DUO range or maybe Oxford Maximiser.
A basic charger that doesn't switch itself off when charging is complete will overcharge and damage most bike batteries within days!