Not sure about the question mark but trunk builds fine for me on windows. That looks like a flex windows error (I have gotten a few of these in the past). Where did you get the version of flex you are using? (unxutils, msys, mingw etc.) I use the version provided with unxutils and once I set the BISON_SIMPLE variable it worked fine.
I just checked out trunk and am trying to build on Windows.
When I try to build the Doxygen project, I get the following error: PRJ0019: A tool returned an error code from "Executing Lex for c:\Doxygen\src\/scanner.cpp ...".
Scanner.cpp has a question mark next to it in Visual Studio. Any ideas what might be causing this?