Hi!

Yes, this behaviour can be explained:
(this is a long posting but full of content, so forgive me)

The N9 (like most other modern handhelds) is powered by LiIon/LiPo battery, and charging the battery is a delicate process. This is made more complicated by the fact that the power is sourced from USB line which has it's own specific quirks; For the USB power to be available both ends need to negotiate and announce each other, only then can the source start providing full current to the sink. If the negotiation fails, the power draw is limited to 200mA as a safety feature.

How this is handled in N9: When USB power is applied, even from a dummy chager, the N9 will boot up the kernel and install the BME drivers to handle the charging. When it is "switched off" the user expects it to be dead, but it cannot be for purpose of charging. This is why, if the device is switched off and connected to a charger, it in reality boots up, but it "pretends to be off", it is in the ACT_DEAD state where it runs but user should think it is off.

Unfortunately ubiboot comes there on the way, and the device which normally would boot the stock Harmattan kernel in ACT_DEAD mode now boots to ubiboot. Ubiboot sees that the USB is connected and enters the repair console, exporting directories over USB and waiting for telnet connection.

This is actually a bug in ubiboot I know of but have not corrected yet, what it should do is to check the startup flags, and if NOLO instructed it to "play dead", then it should start up harmattan in ACT_DEAD mode.

Reason why it's not corrected is that I only now thought about it, since I never charge my own device when it is in poweroff state. (I actually tend not to ever power it off...)

Now, when all power has been drained from the N9 battery, it cannot any longer boot up so much that it would get to charging state.
(actually this is also true of Lumias, and propably other smartphones too, at least I know my son's Nexus7 has trouble charging when it is totally drained)

Luckily, there is simple solution how to fix it, you need to use the flasher to jump-start the battery to 10% capacity, and then connect it to charger to top up the charge.

Instructions can be found, for example here: http://talk.maemo.org/showthread.php?t=87709