Thanks for the lead. I ended up using
HEX(AES_ENCRYPT('JONATHAN', <cfqueryparam cfsqltype="cf_sql_binary" value='#BinaryDecode(thisKey.getKey(), "Base64")#'>))
in mySql to produce the same results as
<cfqueryparam cfsqltype="cf_sql_varchar" value='#Encrypt("JONATHAN", thisKey.getKey(), "AES", "Hex")#'>
And it works great! I didn't have to base64 encode the key - I read somewhere that CF converts the key behind the scenes, which sounded weird, but seems to be true?
Thanks for the help, Peter.