close(STDERR) affects the whole program. There are better ways of suppressing warnings: (best to worse)

• { no warnings 'warningtype'; ... } (Compile- and run-time, specific)
• { no warnings; ... } (Compile- and run-time, broad)
• { local $SIG{__WARN__} = {}; ... } (Run-time, broad)
• { local *STDERR; ... } (Run-time, broad, has side effects.)

And you're only hiding the symptom, not fixing the problem. Like the warning says, a piece of code that should get executed is not getting executed.