Here's what I've experienced with my Bionx kit:

I bought a PL350 with Li battery. All very nice, installed it in my mountain bike. Charged the battery, connected it up to the bike, turned it on. It made all the right beeps however the battery indicator showed only a 3/4 full battery.

I asked Bionx what to do to adjust the indicator, they gave me the list of steps to go through from charging the battery, cooldown period, measuring the battery voltage (41.1V) and then holding down the mode button down for 20 sec. But nothing happened after 20 seconds; nothing even happened after holding it down for 3 minutes. I repeated it many times but the lights would not start flashing faster and the indicator would not adjust. We went several times back to Bionx but they kept insisting that it should work as long as I followed their 5 step procedure with a fully charged battery.

Several weeks passed with he indicator never getting higher than 3/4 full....until yesterday.
I established that Bionx are actually correct in that the battery has to be fully charged before the indicator can be adjusted. What I also have established is that the external charger actually doesn't fully charge the battery. Here is how I found out.

Yesterday, I wanted to get a good workout inside the house so I put the bike in my bike training stand. You know, the back wheel is clamped in a stand and the back wheel rolls against a roller. Prior to this the battery was charged in the normal way with the indicator showing a 3/4 full battery. I turned the Bionx system on and set it in Generation 2 mode. After about 20 minutes I noticed that the battery indication was getting fuller and fuller. I kept going and after about 40 minutes the indicator was completely full. Amazing!
I measured the battery voltage at this point which was 43.3V. This is quite a bit higher than when the battery is "fully" charged by the external charger. The external one only goes up to 41.1V.
I kept biking in Gen 2 mode and noticed that the charing current dropped back and the resistance dropped of too. The battery was now really full. I immediately did the procedure with the mode button holding it for 20 seconds and yep this time it worked. The lights started flashing faster and the indicator shows a full battery.

All this means that the external charger unit never fully charges the battery!

The question is now, what should the battery voltage be when the battery is completely charged by the external charger and is the charger working correctly?

Anyone having any similar issues? Suggestions?