My N900 is not getting charged properly. When I starts charging, it shows blinking red and green light . After sometime it starts charging with continous blinking yellow light . But After that, it stops charging by showing message " Not Charging". Then I unpluggs the charger pin. again I introduce it , I starts charging for some time and again it shows the same message " Not Charging. Rarely, It charge completely.
Is this Software problem ?
Kindly suggest me remedies.

Probably it has a broken usb.
It happened to me some months before, I tried to repair it but made the things worse. Right now I am charging the battery with an old e66 until I will get a new phone
Maybe you can try to open it up and repair it or try other methods, like charging the battery with external charger or with wireless charger(you will not be able to flash your phone though...)

Surely you have a (not yet full) broken USB. So dare to -in near future- you will not be able to charge at all. Or even worse flashing will not be possible anymore.

Immediately install backupmenu and create a backup of rootfs/optfs. This will save you in case of "normal" file system failures or other problems.

Also u-boot and/or recovery console are helpful in case (but do install this only as advanced user with knowledge).

There are few threads about fixing USB ...

Maybe faulty battery or charger . Try with another battery as incompatible or broken battries can throw not charging messages to confirm Or else you need to fasten your usb .

@dermdoc,
There is a recent thread about exactly the same problem. It is usually considered good manners to do a bit of search and post in the existing thread if it does not contain answers you need already, before creating a new thread.

The thread in question is here:
http://talk.maemo.org/showthread.php?t=92854

Post #6 in that thread explains exactly your situation. Just skip the first few lines about top-posting.

In short, as others said before me, your USB port is (partially?) broken. Get it fixed ASAP.