Heh i thought it might be something like that, i translated the url you supplied to use my server and the browser version now works fine, i must say it's superb it does EXACTLY what I want and the formatted ebook is perfect. I'm currently just saving the html file produced by print.php and then converting in calibre to epub.
As for the cli problem I'm using Vista Ultimate 64bit (Though not for much longer I only installed it as a test for some HiDef video encoding and I have to say it's the worst operating system I've used since WinME). I have php_curl and php_tidy enabled in php.ini and also php5.ini just in case it made a difference, I'm also using XAMPP 1.7.0.
The script pulls down the thread but then crashes while converting to epub, this happens every time with any storyid, I've tested those storyids in the browser (Opera 9.64 and IE7 <shudder>) and they work perfectly.
Here's a random one I've just tried including the commandline just in case I'm doing something wrong there:
"C:\xampp\php\php.exe" "C:\xampp\htdocs\flag\fflag" -s ffnet -i 4740107 -f epub -o c:\temp\test.epub
Every ID I try gives the error below:
Problem Event Name: APPCRASH
Application Name: php.exe
Application Version: 22.214.171.124
Application Timestamp: 493d760b
Fault Module Name: ntdll.dll
Fault Module Version: 6.0.6001.18000
Fault Module Timestamp: 4791a783
Exception Code: c0000005
Exception Offset: 0002f217
OS Version: 6.0.6001.2.1.0.256.1
Locale ID: 2057
Additional Information 1: fd00
Additional Information 2: ea6f5fe8924aaa756324d57f87834160
Additional Information 3: fd00
Additional Information 4: ea6f5fe8924aaa756324d57f87834160
Hope this helps though I would have to say it's something on my end as it happens with every storyid. I'll be going back to WinXP shortly so hopefully that will solve the problems anyway.