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I have a gui shell for my application, using wxPerl... when the GUI application is linked as a textmode app
Your gui is a compiled executable?
And by "linked as a textmode application", you mean you use /SUBSYSTEM:console when building the executable?
What linker options are you using when you "linked as a GUI app"?
If you are using /SUBSYSTEM:windows, then that might start to explain your symptoms (MSVC link.exe docs):
WINDOWS Application does not require a console, probably because it creates its own windows for interaction with the user.
Note: that "Application does not require a console," means when the application is loaded, no console is allocated to it. Of itself that is probably not a problem, but it ccan also mean that processes started by that application may inherit that trait.
if I don't link the UI as a gui application, then when launched from the gui windows explorer, the textmode box appears when the gui is started instead..
Probably your best solution would be to drop IPC::Run3 (on Windows at least), and use Win32::Process to start your subprocess(es).
This has options to control the creation of consoles (CREATE_NEW_CONSOLE) and console windows (CREATE_NO_WINDOW) and background processes (DETACHED_PROCESS) etc.
It's not clear to me how you are creating your perl application as a linked executable, so this is more a list of things to investigate rather than a definitive solution.
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