Okay, as far as I can see, the issue is not with Python, but that lldb.exe and liblldb.dll have their own private copies of the CRT.
When startup script is given on the command line, lldb.exe creates a pipe, writes the script into the write end, wraps a stdio file around the read end, and gives the resulting FILE* to SBDebugger::SetInputFileHandle(). Unfortunately, since SBDebugger lives in liblldb.dll, with its own copy of the CRT, that handle is not valid there. Later, it tries to read from that handle, and... boom.
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