Just to comment and provide some closure to this, in case anyone looks, recall that my seeming issue was this:

1. Client connects to server and does some i/o
2. 2nd Client attempts to connect to server and do some i/o. It spews a few lines of text at the socket and waits.
3. Server finishes with client #1, accepts() client #2
4. Not all the text send over in #2 is there.

Well, this is under Windows (Cygwin to exact) and I found the issue... during the negotiation between client and server multiple debugging output is done. In the DebugMsg() function is the following:

    chomp(my $d = `date "+%Y-%m-%d-%H.%M.%S"`);

That is the culprit. Shelling out and running date is somehow flushing/truncating the sockets. A simple change from that to

        my $d = strftime("%Y-%m-%d-%H:%M:%S",localtime(time));

Completely fixed my issue.

Pain in the ass, eh?