To install flasher, do

sudo dpkg -i --force-architecture maemo_flasher-3.5_2.5.2.2_i386.deb

afterwards, install ia32-libs from multiverse:

sudo apt-get install ia32-libs

Before installing ia32-libs flasher kept telling me this:

ubuntu@ubuntu:~/Desktop$ flasher-3.5
bash: /usr/bin/flasher-3.5: No such file or directory

Now, to flash PR1.2 and the vanilla eMMC content, issue the following two commands:

sudo flasher-3.5 -F RX-51_2009SE_10.2010.19-1_PR_COMBINED_MR0_ARM.bin -f
sudo flasher-3.5 -F RX-51_2009SE_10.2010.13-2.VANILLA_PR_EMMC_MR0_ARM.bin -f -R

This will flash and reboot after flashing the eMMC contents.