It is possible that Apache being run as a service does not have the correct permissons to do something.
The default user running the service will be "Local System Account". You can change this on the Log On tab of the Service properties dialog.
For example try changing this to the same user that you are logged in as when running from the command prompt. You will need to restart apache, for this to take affect.
Hope this helps, Gerard.
Update: It really all depends on what your external program is trying to do, and how things are set up there... I haven't had similar problems, but have avioded them, when scripts are trying to access the local network for example.
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