I left this waiting for someone from the more regular windows users to answer. Sorry Greg, you have waited long enough...
I am not sure if things have changed in 12 but FileMaker PHP stuff was stored in the Program/FileMaker Server/Web Publishing/php (ish) path.
This is ok for a 1 machine configuration, but for 2 machine configs you have to (at least on a a Mac) also install the standalone FileMakerAPI... a copy of which is probably in the web Publishing Directory.
That is why the IWP works and the CWP doesn't. They are both using the same WPE but not the same copy of the API.
On a single install, you just have to generically include the filemaker.php which includes the FileMaker servers version so there is no need to install the API whereas the other machine knows nothing about FileMaker other than what you install.
Hope that makes sense...
(I am mostly a Mac person and I do installs and setups on windows then don't look at them again so I forget the specifics)
Is this a 64bit server by any chance? I've had trouble in the past deploying CWP on Windows 2003 64bit (works fine on 32bit Windows 2003 or 64bit Windows 2008).
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