So this is how things went wrong:

My phone was working fine 3 days ago. After installing some apps, including backupmenu and uboot, I rebooted. After that I cannot boot into maemo anymore. The phone went into reboot loop when I tried to boot "attached kernel".

So I thought maybe something was wrong with the kernel. What I've tried so far:

1/Reflash the kernel only.
2/Reflash rootfs with pr 1.3.1 firmware.
3/Reflash rootfs with pr 1.3 firmware.
4/Reflash both EMMC and rootfs.
All done in Ubuntu. Flashing attemps returned no error. But didn't work.

I've also tried to fsck the partitions in ubuntu 12.10 (first I tried this, but mass storage didn't work, then I tried this and it worked). First it returned some errors about bad blocks, but after running fsck -af a few times it returned no more error. I also formatted the partitions using mkfs.vfat /dev/sdb1 and mkfs.ext3 /dev/sdb2 (n900 is mounted in /dev/sdb)

Battery was well charged (using charging script in rescueOS).

After doing all the stuff above I flashed both EMMC and rootfs once again, but it still didn't work.

The booting behavior is the same: nokia screen, then 5 dots running back and forth for a while, and then shutdown.

I'm already running out of idea what to try next. I've always thought reflashing both EMMC and rootfs can solve everything. Now apparently it's not true in my case.

Any idea or advice for me? I've been struggling with my N900 almost for the whole past 2 days already.

Did you flash first vanilla (eMMC) and then combined (rootfs/optfs)? (which is the recommended way!)

If not, then try this out.

If yes, then try this
flash combined
then flash Vanilla (eMMC)
flash again combined

Be sure to not restart device within this sequence (do NOT use -R option).

I always flash EMMC first (no -R), then take battery out, then rootfs.

So for your suggestion, I did this if I understand it correctly:
_flash combined (no -R)
_continue flash vanilla (no -R)
_take battery out
_flash combined again

The result is still the same.

Can the battery be the cause anyhow? When I was playing around with rescueOS, I noticed sometime I got sudden shutdown. Moreover when I took battery out and put back in, the phone can't boot straight away. I had to adjust the battery position a bit (sliding over it back and forth). I think it may be somehow loose. But the battery is still functioning, so I really don't know what's wrong with it.

when in reboot loop, sometimes, removing the battery for some minutes the trying again keeping pressed the power on button until white led goes off may help...
anyway, check the battery voltage..

you could also try a rescue boot (to check the phone's life status) with:

talk.maemo.org/showthread.php?t=75369

It happened to me too.In my case battery was not good.I found the cause when I inserted my battery in Nokia 5800.Try to adjust the pins on the battery or try with another one.

After what you described I would start looking for another battery.

Agreed.

After you may have tried out to charge the batt for a few hours attached to wall charger (after flashed).
Did you try to charge it that way after flash? Or start to boot directly after flash?

Long shot but try to boot off the battery then plug the wall charger in at the 5 dots. Maybe able to hold enough juice in the battery to boot.

Try enabling r-d mode. If that doesn't work, flash framebuffer kernel, take a photo of the output before it turns off and post here.

Install Flasher 3.5
Download libusb-win32-bin-1.2.2.0.zip - http://sourceforge.net/projects/libusb-win32/
Press U while starting N900 and attach USB
Wait for the original driver to install.
Run inf-wizard.exe (bin folder in zip) - Run as Administrator

Press "Next"
Search in list and select "0x0421 - 0x0105 - Nokia N900 (Update Mode)"
Press "Next"
Press "Next"
Save .inf file
Press "Install Now"
Press "Install this driver software anyway" on warning message.
You should get "Installation successful." and press OK.

Check Windows Device Manager for "libusb-win32 devices", expand and verify "Nokia N900 (Update Mode)" can be found.
Now you are ready to run Flasher 3.5 with your parameters. every time u fail u must load lib-usb again !

IF THIS FAILS ! : figure out somehow ( pull patery, insert whit preset button and cable) PC or lib-usb must detect n900 so you need download few drivers and if u will fail ENABLE RD mode in your flasher by comand : ./flasher.exe --enable-rd-mode and do it all again
u wellcome !