One thing that also took me a long time to realize with the original battery in my Harmony One is that with these rechargeable Lithium batteries you have to practically run them down to almost nothing before you recharge it again otherwise if you place the remote back in the charger every time you are not using it, it prematurely starts to lose its ability to hold the charge for any length of time. I was making the mistake of doing the above and it got to the point that within a year it wouldn't hold its charge for more than a few hours and I had to replace the battery before its time.
I hate to say it, but that is a myth carried over from Ni-Cd days. Lithium batteries are designed to NOT behave that way. No "memory" issues, no need to "drain and recharge" multiple times just to get things back to normal. In fact, if you you drain a lithium batter too far, you will actually destroy the battery.
There are other issues probably with your remote such as it not registering that the battery is not 100%, or something, or the battery has been damaged, or just worn out. I only say this so that people don't try to start draining and then charging their lithium powered devices and in turn end up actually reducing the life of their battery or destroying it by over-draining it.
