I looked through the MX-3000 programming manual (BTW, you can also find a copy by Google-ing "MX-3000 programming", if you don't have one already). There is a good discussion in the manual about how to successfully learn the IR for difficult buttons (key).

Since I haven't programmed an MX-3000, I can tell you that on the 6000 and the 980, I can program as many buttons (hard or soft) do the same thing as another button. I have a few cases where I have a soft button duplicate the hard key functionality. So, nothing you said concerns me. On the LCD, when programming multiple volume controls, I usually make sure each soft key specifies which volume control (such as "4DTV Vol +" so I don't confuse anyone using the remote (or at least limit any confusion).

The hard keys always control the same volume control (whether that be a TV or an A/V receiver) - in other words from page to page on each remote, the meaning of the hard key volume/mute don't change. It's good practice and really reduces the frustration level.

Bottom line is the remote doesn't really "know" what you are programming, it just sends out the codes you told it to.

The explanation in the "IR learning" section of the MX-3000 programming manual is very good (I think they had three different techniques) and I think reprogramming may solve your volume control issue. The manual also stresses the importance of testing all of the learned buttons before moving to the next step.

Try this (my last attempt at describing this):
With the remote hooked up to your PC

1. click on a button that you want to learn

2. in the bottom window (where IR data or macros exist) double click on the white area directly below the header of the column called "IR data". Alternatively you can also click on the IR data icon on the tool bar of the this window.

3. this brings up the "IR data" dialog box. Click on the expand button on the right.

4. Get your factory remote ready and when ready, click on the learn button on the right. Press the button on the original remote that you are wanting to lean and it should say "Learned" or good" (something to that effect).

5. Now click on the "Register" button. Yes, that's right, the "Register" button you said doesn't exist.

6. Now click on the OK button which will close the IR Data dialog box.

You should now have a small blue "L" on the button you just learned.