krmr, if you are on Vista heres what you need to do...
First, Florian is right, any file paths with a space (eg: Program Files) in them need "quotes around the filepath".
so open your bat with a text editor and change
SET PDF2SWF=C:\SWFTools\pdf2swf.exe to...
SET PDF2SWF="C:\Program Files\SWFTools\pdf2swf.exe"(i know you've done this, but i'll outline all steps)

Next, you can't just click on the .bat
You need to do the following:
Open cmd.exe as an administrator. It live in C:\Windows\System 32\cmd.exe
You may need to right click it and "run as an administrator".
If all is good you should see at the top of it
Administrator:cmd.exe
The prompt you see should say
C:\Windows\System 32>_
I'd now make a directory in C: (eg: C:\megazine) and put a subdirectory in megazine (eg: C:\megazine\src).
Put your bat and your pdf into C:\megazine
C:\megazine\src is where your swfs will be written to.
You now need to change Directory in cmd.exe to where your pdf2megazine.bat is.
This is because in Vista the working directory is where cmd.exe is running from, NOT where the bat is
Type in
cd C:\megazine
, hit enter.
The prompt should now be
C:\megazine>_
Now type for instance
pdf2megazine.bat theNameofYourPdf.pdf "src/page" 12 600 900 hit enter.
This gives you 12 swfs called page1.swf,page2.swf etc(one for each pdf page) written to C:\megazine\src and a megazine.xml file written to C:\megazine that tells all swfs to display at 600px wide and 900 high and sets the swfs paths to "src/page1.swf" etc
Furthur command parameters are in the bat file.
Be careful with your / and \ characters.
Vista can be a pain
