The battery management software has decade of legacy in it

The measuring relies on two crucial things: BSI (Battery size indicator), which is a resistor through the third pin on the battery, And the battery's true capacity.
If the two deviate too much, the battery state tracking gets thrown too far off, resulting in sudden big corrections.

The two (BSI and battery actual capacity) can disagree in some third party batteries, or if battery has aged significantly giving it lower capacity and higher internal resistance, or if there's poor conductivity between battery contacts on the battery and the battery terminals on the phone (dirt, corrosion, etc).

When charging, the software is very reluctant to admit/reveal if charge rate is lower than discharge rate. And, when it does, you probably miss the notification anyway. The response to input undervoltage conditions is to check whether voltage on input port still exists, and if so, retry charge at lower rate.
Thus, a power adapter unable to supply enough current, a damaged cable, excessive resistance at the connector (dirt, corrosion, too loose mechanically, etc) can cause charge rates below normal. A loose USB port can cause intermittent errors which can be misinterpreted as a weak charger. Multiple repeated intermittent connection issues in a short period of time can cause even stranger issues, such as the hardware chip resewtting itself to failsafe defaults, which results in a partial slow charge at best.
Again, connectivity issues between battery and phone can cause charging issues just as well as connectivity issues on input.

In the case of Solid orange light, there is no software running at all. The hw chip is doing an independent charge until there's enough power to boot. This should only happen if one disables bme and runs the device beyond the normal cutoff. If you reach such a situation, it's indicitative of a faulty battery or parasitic constant drain in the device itself. Also after prolonged periods at empty battery with the battery stored in N900 you'd see a few seconds of solid orange, that would be normal-ish. If it doesn't recover from Solid Orange to the next stage (which would see the solid orange replaced by glowing orange and/or reboots), it would in addition to the possibilities of parasitic drain and bad battery mentioned before also be a possible fault in the DC adapter, cables, port or N900. Further measurements and troubleshooting would be required.