Couple of pointers which may or may not help. First, I run IIS4 on NT4 SP5, so your mileage may vary if you're at a different Service Pack level.
The MSVCRT.DLL that came with the PHP v4.0.2 distribution is newer than the one on my box in \WINNT\SYSTEM32, so I renamed the one currently there (from a command prompt as through the GUI NT won't let you modify the file claiming it's "in use") to something like MSVCRT.DLL.OLD, then copied in the one from the distribution. Yes, if you still have the older MSVCRT.DLL file installed, this could be part of the problem.
I don't run the ISAPI module but rather have the CGI (.EXE) version configured due to issues still lingering in the ISAPI module regarding session management (i.e., it doesn't work right).
Also, when posting a problem, please provide as much information as possible, such as any error messages you receive and the PHP code you were trying to run. This helps enormously in that others can try that code to see if it is working on their machines. You wrote that it is "a PHP file containing a single line". What is that single line?
Anyway, I know it's not much, but hopefully this will help. I understand the desire to use the ISAPI module (I'd like to do so myself, as I'm not keen on running CGIs which load/unload memory all the time), but I just wanted you to know there there ARE still issues in the ISAPI, at least regarding session management (which is what my projects involve).