Maybe this will help you:

With the whisper system you can direct (from your master) your slave toon to whisper someone using the @toonname segment.

So, for your macros, where you whisper from the master to the slaves, you can change those to direct the redirect whisper back to the master and not to the last person the slave whispered.

I assume in your macro, you currently have:

/w Slave_Name My message here

If you change it to:

/w Slave_Name @Master_Name My message here

Then your slave will whisper the message back to your master, rather than bothering someone else.

Make sure that the @Slave_Name is the first part of your message and there is no whitespace in front of the @.

If you try this, please let me know if it works for you and solves your problem.