I tried xnview with no joy.  Haven't tried the others, and certainly not any command line aspects as that didn't occur to me.  I would prefer a simple program to solve the problem because I can then offer this to my colleague and whoever else needs to save such files for posterity.
It would also save paper because the first thing my colleague does it to print them out - and we often get long listings, bank statements etc which could be viewed onscreen.

Three other possible options to look at before you get too deep into coding a custom solution:

http://www.xnview.com/ - similary to Irfanview but IMHO superior, try batch processing
http://www.imagemagick.org/script/index.php - a powerful commandline image processing library/system
http://djv.sourceforge.net/ - try DJV_convert.exe and commandline options, designed to deal with complex images for visual effects, which often have layers, so it may automagically do what you want

- Oshyan

-JavaJones (July 01, 2010, 12:32 AM)

Thanks skwire, that's looking neat.  I have forwarded the email i get when i receive a fax.  Funnily enough i managed to fax it the right way around the first time, so i had to refax it again to get it wrong :)  
What this proves is that everyone we know can't load a fax machine correctly!

Here's where I am now...
 (see attachment in previous post)

-skwire (June 30, 2010, 09:40 AM)

1) Yes they are all mis-rotated, i.e always upside down.  If I get a 20 page document it's annoying.
2) yes one TIFF at a time.  I download it then usually have to print it off as I can then actually view them without much pain.
3)  I can arrange to supply one of them - how should I get it to you?

-skwire (June 30, 2010, 06:55 AM)

1) Great, that makes things easier to deal with.
2) Okay.  However, would you like this app designed so that you could handle multiple TIFF files in a batch?  Or is a single-use type of design more what you're after?
3) You can try attaching it in a PM to me.  Failing that, you can try emailing to [email protected] or [email protected].

Thanks.