Prompting compile command issue in Project

I'm using an MKS change management tool to, among the other things it does,
compile objects in Rdi 7.1 (aka. WDSC). When I prompt and run the MKS
compile command from RSE, I get the Error List window right away. I have
to prompt first, which I'll explain later. When I prompt and run the exact
same command in an i5/OS Project, I get no results. Its not exactly the
same command, because the prompting seems to work differently in a Project.

The MKS compile command returns the create command it will use, as a
command string using a prompt override program. Prompting the compile
command in RSE seems to run this Prompt override program just fine, as it
pulls in the correct create command with all the special trimmings.
However, if I prompt this exact same command over source in an i5/OS
Project in RDi, the prompt override program doesn't seem to run, or maybe
it fails.

I cannot figure out why a Project would behave differently than on an RSE
member. If I manually type in the create command into MKS's ICOMPPDM
command, then I do get the error list back immediately. Also, I am running
both compiles interactively from RDi point of view, so I don't think this
is a case of a batch vs. interactive problem.