I've been frustrated by this for a while and these are the main problems I've ran into:

1. There are a LOT of crappy chargers and cables out there. You will have to hunt for good ones. Don't trust the badge that it's a good charger/cable
2. A broken USB port can't be fixed by buying a new charger/cable.
3. The default BME does do the right thing, as far as I have seen. Though it will not let you use the last bits of power from your battery, it will try to lengthen the overall lifespan of the battery and any chargers hooked up to it.

I've been buying chargers and charger cables to see what actually works and what doesn't, with mixed results. Right now I have exactly one good wall charger, made by LG (5.1V 700mA), and its cable. I also have exactly one good charging/data cable, which was made by Nokia (CA-101D, the 8cm short cable). Every single other charger/cable I have is lacking, including my Nokia AC10C, whether it be due to poor construction, or wear.

I even recently bought one of those phony A1265s chargers (the little cube Apple charger) to see how bad they really were, and let me tell you, these do indeed suck. Though it says 5V 1A it can't really supply that much before it starts drooping a lot.

I would suggest people should be careful when using those special charger scripts. BME is trying its best not to fry USB ports and cause a fire, but yes it can guess wrong and tends to be pessimistic (some USB hubs can supply all the current that the N900 needs, but since it does not have D+/D- shorted, the N900 won't try.)