+ to the title:
When the battery (not original, capacity 1100 mAh) dicharges and I plug the charger in, the yellow light just keeps on (not blinking) for around 10 minutes, and then it does nothing and won't turn on.
BTW i have CSSU version 21.2011.38-1Smaemo6.1 and the port is not original, it has been changed 2 times.

From your description, the most obvious culprit seems to be the battery. Is this the first time you are charging it? Was it completely dead before you put it on the charger? Does the phone work with any other battery? Can you charge it offline (out of the phone, with a stand-alone charger, for example one that came with your digital camera)?

Not charging it for the first time, I use that battery for about a year (I remembered to ask about it just now :-)
Wasn't completely dead, works good when it has at least a little charge in it. Works the same with an original Nokia battery
About standalone charger -- I don't have one :-)

Sorry about the confusion, by "completely dead" I meant "completely empty".

But now I am confused too. Let me see if I get it right. Your phone works fine unless the battery is fully discharged. When it is, it does not boot up. That is nothing surprising, you need to let it charge a bit (10 minutes should be OK) before you turn it on.

If that does not work, then it must be your USB port. Too much resistance either on the contacts or the solder pads results in too much voltage drop when the charging current is highest, such as when the battery is empty. The fix would be fixing the port, but an easier workaround would be never letting the battery discharge completely and/or invest in one of these.

Thanx a lot. And what do you mean by "fixing" it?

Re-solder it. Clean it. Replace it. Depending on the exact nature of the problem.

On a stock N900 isn't the emergency charge mode a very low mA load which engages and gives the steady(vs pulsing) amber notification light? It is when there is so little battery the phone is unable to even boot into a smart charging mode. From what I remember from here on TMO the phone will need something like overnight to just have enough battery power to boot into the smart charge mode and begin normal charging if that even works. Best bet is to get an external charger for these 'jump start' type situations where the phone is left dead and helpless, the OpenMoko GTA02 had a similar situation.
http://www.amazon.com/TOOGOO-Battery.../dp/B00FFYLSE8
I would suggest waiting on any solder solution as that could easily ruin a working USB port.

OK, and what is a "stock N900"?

As far as I know there has never been a hacked or open source bootloader released so all N900s are in the stock configuration except for perhaps changing the Nokia logo seen at bootup.

The N900 needs to be "on" to charge. this means a completely dead battery will not charge in the device.
"on" doesn't necessarily mean booted up BTW, there is a state called "ACT_DEAD" in which, the device can charge but the device is "off" not booted.

If you get a solid yellow this normally means the battery is very low but can be charged, you should leave the device to either boot up on it's own or pulse yellow before booting up the device.

It will also not switch on with no battery.

I would consider a good quality new battery if you haven't replaced it in a while, Li-ion batteries don't last forever. Especially, if you run them completely flat.