I might be able to shed some light on your problem. This happens to me too. The good news is your charger isn't malfunctioning. But first a very quick explanation of what's going on with your batteries.
NiMH shouldn't be discharged below approx 1.0 volts, and never below .8 volts. Normally, an electronic device automatically stops working when its batteries reach 1.0v per cell-- especially more sophisticated electronic devices. This prevents over-discharging your batteries. Say you have device that takes 4 AA. If one or more of the batteries run out of charge long before the others something called reverse charging can happen where the remaining good batteries damage the one that ran out of charge. No two batteries are identical to begin with but as they age their capacity declines. This is why you should use batteries of the same capacity, age, and charge (not some fully charge, some partially charged). Also, some devices, not designed with NiMH in mind, like toys designed for Alkaline will just over-discharge the cells.
In the end you wind up with one or more batteries that has a really low voltage and when you stick it in your really nice expensive charger, it detects something is wrong and doesn't risk charging it. Paradoxically, if you put this battery in a "dumb" charger for about 10 minutes, it will revive it enough to be charged by your "smart charger". The only way to avoid having to do this is to not run the batteries all the way down. While this is a bit of a pain, it will significantly prolong the life of your cells.