I finally figured it out. Running from a shell was ****ing me off because my usb devices just arent being started when explorer.exe is not running, and it's a pain to re-initialize explorer if you need to fix something. So I went about it a different way:
1- Download and install a free program called Startup Control Panel.
Set Roadrunner (or your frontend of choice) as a startup program.
2- Get rid of desktop icons. I did this using a registry hack:
If I need to get to a program, I just use the start button on the taskbar, (which is set to auto-hide) Then I set the desktop background color to black.
When the computer starts, I get the VIA bios logo, then black screen, then roadrunner pops up and music begins to play. I also set "hide taskbar", "hide desktop" and "hide pointer" in the RRconfig settings.
All my usb devices work, and I can get into windows easily.