I get the same for both.

D:\>perl -MDigest::MD5 -e "print Digest::MD5->new->add(<>)->digest" md
+5 japh.pl
Can't open md5: No such file or directory at -e line 1.
hi-bit-string

D:\>foo.bat md5 japh.pl
hi-bit-string
[download]

Is the file you are using named something with spaces? If so you have to encase the name (and %2) in quotes to propagate the spaces. Also, there is no %1 in your example. Sample output and input files could have been useful as well.

--
perl -pew "s/\b;([mnst])/'$1/g"