For verification use some sort of message verification algorithm, like a checksum or a signature. Check out String::CRC32 for an example of such an algorithm. Or Digest::MD5, if you'd prefer something like that.

This is good practice no matter what, partly just so that you can ensure that there's no tampering with your messages.

For the problem of not reading the socket correctly: how are you reading from the socket? You could try using sysread and syswrite. That's what I'm doing, and it works great.

If you'd like an example of some of this, check out (shameless plug) the packet code in Net::SSH::Perl, my Perl implementation of an ssh client. SSH network packets are encrypted and contain message verification (in the form of checksums), so you might get some ideas there. The packet code is in Net::SSH::Perl::Packet.