Those "special characters" are the nature of Base 64 encoding, use md5_hex instead.

From the docs:

md5_hex($data,...)
           Same as md5(), but will return the digest in hexadecimal form. The length of the returned string
           will be 32 and it will only contain characters from this set: '0'..'9' and 'a'..'f'.

But chances are how you're comparing the digested strings is wrong because a forward slash shouldn't break it. . . Let me guess- you're doing the comparison with DBI, but you're not using placeholders?