I too, am a user that was plagued by Input Remapper not saving my settings and having to re-set them each time I boot. I found a workaround using a batch file that allows you to save your settings. These instructions are for XP, but should be similiar on Vista.

1. Completely uninstall Input Remapper.
2. Install Input Remapper, make sure the tray icon option is unchecked during install.
3. Start the Services Control Panel. This is located in Start > Control Panel > Administrative Tools > Services. Select Input Remapper in the list, and then go to Action > Properties in the menu at the top. Under "Startup type" on the "General" tab, set this to "Manual".
4. Start the Input Remapper tray icon from the Start menu, right click on the IR icon in your system tray, and set the keyboard and other settings the way you want them. This will create a new settings file.
5. Navigate your file manager to C:\Program Files\Input Remapper. Make a copy of the file "Settings.dat" and name it "Settings.bk"
6. Create a new batch file, call it "Input Remapper.bat"
7. Edit the batch file and add these lines:
   
   CODE
   @echo off
       cd "C:\Program Files\Input Remapper"
       copy Settings.bk Settings.dat
       net start "Input Remapper"
8. Create a shortcut to this batch file and place it in your Startup group in your Start Menu programs list (right click on the Start menu and click Open to edit the Start menu).
9. Now when you reboot, a DOS window will appear briefly to copy over the settings file and start the Input Remapper service. If you want the tray icon back, you can add
   
   CODE
   "C:\Program Files\Input Remapper\InputRemapper" -TrayIcon
   
   to the batch file. Furthermore, you can hide the DOS window entirely on boot by downloading the free Hidden Start utility, extracting it to your C:\Windows\System32 directory, then modifying the shortcut for the Input Remapper batch file by going to the shortcut's properties and changing the shortcut target to:
   
   CODE
   hstart.exe /nowindow "C:\Program Files\Input Remapper\Input Remapper.bat"

I hope this helps. I was pulling my hair out trying to solve this annoying problem and now that I found a solution I wanted to share it with all of you to save you from all the frustration.

ahh thank you so much, it was extremely annoying to have that reset every time I rebooted.

works like a charm!

I'm having a really hard time reproducing this error. Any more information about reproducing it would be great. It does not seem to happen for me when I enable user account control.

Can this post be made sticky? I see that a lot of users are still having this common problem.