You haven't shown us the printf output; should we assume that the filenames are being printed out all right?

Even so, it might have been better to use /\.\Q$filetype\E$/ in the regex rather than /^[\d\w\s]+\.$filetype/, for a variety of reasons. For one thing, it will ensure no nastiness after the ".xls" in the filename. It's a longshot, but barely possible.

On another note,

my $Book = $Excel->Workbooks->Open($files[$x]) or die " $! ";
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is much better than

my $Book = $Excel->Workbooks->Open($files[$x]) || die " $! ";
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in general. But I doubt that it's your problem here.

buckaduck