>I know that macro-subbing can prevent a program being pulled in to the project manager. If I use macro-subbing in one case and directly call the routine elsewhere, will that prevent it too?

Any indirect call will hide a called program from the Project Manger, not just macro-substitution. For example

lcProgName = "Whatever"
DO (lcProgName)

Any direct call makes program known to the Project Manger regardless of any indirect calls

>
>I know referencing an array in a report will always generate an error during compilation or rebuilding, even if EXTERNAL ARRAY is used.

VFP cannot distinguish between array and function. If you would have a PRG with the same name it'll be pulled in.

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>What other things would cause the project manager rebuild to fail to include a program?

I don't remember anything else that would prevent the Project Manger from pulling a program in.