though they should be closed implicitly anyway, shouldn't they,
Only if you use lexical variables as file handles. If you use open HANDLE, '>', $file;, then HANDLE is a global that doesn't go out of scope.
When a file is closed, it should be written to disk immediately (well, the OS can still cache it, but it has to do it transparently).
What you describe here should never happen, so if you can reproduce this behaviour in a small, self-contained script, please file a bug report.
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