If you haven't configured CPU Affinity through ISBoxer, go to each Slot in your Character Set and assign EQ a different CPU core per slot (just rotate between cores). If all of the cores are selected, that's fine -- that leaves it up to Windows to do the load balancing. If no cores are selected, the CPU Affinity selected by the game itself (if it does at all) is used.
Beyond that, I can give you a solution. Whether you like it or not is another thing

You may already be familiar with it.
EQPlayNice has a feature called Rendering Limiting. This can be used in conjunction with IS and ISBoxer (just make sure to turn EQPN's FPS limiter off so you can use the one built into IS and configured through ISBoxer). What this feature does is prevent the game from rendering the world every frame when in the background. This will reduce both CPU and GPU usage in EQ1. However, it comes at a cost -- not rendering the world every frame means the game will appear choppy, and since this feature lets the UI render, it will appear to flicker/flash when the game is allowed to render the world. A lot of people interpret this as lag, however it is allowing the game to run at an increased framerate (higher FPS), while reducing CPU and GPU consumption. As another helpful benefit, autofollow performance in EQ1 is based on your framerate, so autofollow should be smoother.
The easiest way to try this with ISBoxer is as follows:
1. Install WinEQ 2
2. Run WinEQ 2 -- if you're on Windows Vista or Windows 7, you will need to right click and select Run as Administrator or it will NOT work with IS/ISBoxer, and in fact you might get a -20 error from the patcher (I have not updated WinEQ 2 to elevate the patcher to admin)
3. Right click the WinEQ 2 icon in the system tray and select Preferences from the Options submenu
4. Expand EQPlayNice in the Prefs. window, and under both Foreground and Background set CPU/FPS Limiter Mode to FPS Limiter and put the CPU/FPS Limit at 100 or more
5. Under Background, the Rendering Limiter Mode should be 1 out of x frames. Rendering Limit can be whatever you please, default is 30 meaning that 1 out of 30 frames will render the game world -- If you get 30 FPS, the game world will update once per second in the background windows. If you want it to flicker faster, drop the number down. If you want it to flicker slower, raise it higher. The lower the number, the more you will be able to see happening in that window besides the UI (which will continue to render each frame)