The Siemens FC5/FC6 blocks are used for sending and receiving custom TCP messages. They don't use a special Siemens protocol. If your co-workers have documented the protocol, you may use socket communication in scripting. There are some forum threads (e.g. this one) about this.
Yes, i would also be worried. But that is a general problem with your concept. With operating system timing and enthernet connections involved, it is a bad idea to rely on communication times. Make your system stable by design, e.g. by putting the tracking logic in the plc or by some kind of handshaking.