Maybe a stupid question but although you can do it, is there a reason you need to get the published app to run another published app? Otherwise, the first app should be able to launch the second app same way as it does on a published desktop.
For example, assuming you haven't locked the server down, publish something like "notepad.exe", then run that published app and then do a file/open and find something like - for example - c:\windows\system32\winmine.exe and (from within the notepad file open dialog box) right click on it and choose "open" - it should spawn minesweeper.
Sometimes there can be confusion when (say) the published app is anonymous whilst the desktop is authenticated which is why it works in one but not the other because of authentication/security issues...... there is also a bug I recall in one version of Metaframe where a spawned app wouldn't appear, but there's a patch available for that from support.citrix.com and anyhow it doesn't sound like you're seeing that.
Cheers