Regarding your follow up questions:

which (Windows) build systems would be affected?

I'm pretty sure ANY windows builds are affected, as this is an OS level thing. Which is to say even mingw, which has a slightly differently named flag (-console?), but has the same effect IIRC.

we could build two different executables (fluid and fluidc?).

Yes, a separate exec seems the only solution I think. See my reply above regarding details. I think fluid-cmd would be clearer; this is what I've seen other commercial apps do that run into the same problem, and I've used it too.
The only way to avoid a name change is to make separate directories, e.g. windows/fluid.exe and console/fluid.exe, but that can lead to confusion I think.

Note there are ways in DOS to start a windows app and wait for it to finish and get its exit code, namely:

    start /WAIT fluid -c bla.fl

(But that doesn't solve the stdin/out/error problem.)

Re: your follow up comment to me about WIN32 affecting SUBSYSTEM, ya my edit and your reply crossed in time; I read back your first response and saw that was the effect.

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