hi

and welcome to Maemo!

there really isn't much to install
simply download the latest flasher version from the same directory (ftp server) where you find the firmware
unpack it (tar.gz if memory serves well)
if that's where you have problems, simply install MC (Midnight Commander) (outstanding must have file system troubleshooting tool for any GNU / Linux comp.; it will also open most archives (RAR, ZIP, TAR.GZ) unless they are compressed with some nutty tool (7z to name but one )
and it comes also for Maemo )
once you have unpacked it to a directory
say /rpm/maemo_flasher-3.5_2.5.2.2
simply copy the firmware into the same directory

• power off N900
• to flash only the root file system (thus PROGRAMS only, leaving your data in MyDocs untouched)
  

  cd /rpm/maemo_flasher-3.5_2.5.2.2
  ./flasher-3.5 -F RX-51_2009SE_20.2010.36-2_PR_COMBINED_MR0_ARM.bin -f -R

• quite a few lines will appear ending with something like
  no device found; waiting...
• connect USB cable to N900
• open keyboard and press & hold U key (ON THE N900!)
• connect USB cable to PC
• once flasher-3.5 starts doing its job you can let go of the U key

if you wish to flash all the settings & erase personal data (maybe needed if device is acting very strangely, like in your case
backup all your data on MyDocs (whatever you called your N900 in the file manager) either to a micro SD(HC) card or to your computer and use the following flasher-3.5 command before the above one:

• ./flasher-3.5 -F RX-51_2009SE_10.2010.13-2.VANILLA_PR_EMMC_MR0_ARM.bin -f

(the remaining instructions are identical)

hth