Everything your saying suggests that you shouldn't have a problem. This stuff happens from time to time though. Weird problems I've had in the past that nobody else could figure out. Sometimes you just got to start over.
I suggest deleting everything for this emulator... the emu, the saves in E:\, and anything in the T and U data folders.
Get a fresh copy of the emu and FTP it over again.
Kind of a pain I know, because you have all of your roms in the "roms" folder in the emulator directory. That's why I seperated all of my roms from my emulators. My roms for Surreal are in "F:\Roms\Nintendo\N64". Where you have them shouldn't matter though as far as the emu is concerned as long as your .ini file is pointing to the right place.
What is your free space on your drive? Since you've got this all on your E:\ drive I'm assuming you didn't put in a bigger hard drive. You might be suffering from weird problems due to space issues. You should never get anywhere near max capacity on your E:\ drive or all sorts of weird things start happening. Most N64 games don't work very well anyhow, so I suggest just putting on a few you would like to try and deleting the rest. (There is a compatibility thread on the Surreal in here to help you decide which ones you'd like to put on the XBox). Mario 64 and Mario Kart 64 pretty much work flawlessly, so you could delete everything else and try those for testing first.
RMM's suggestion for zipping your N64 roms is also is a great idea if you didn't upgrade the hard drive. You need all the space you can get. Be sure to zip them in .zip format in Winzip though. Surreal won't read them in .rar or 7-zip files.
Good luck.
This post has been edited by ressurectionx: Jan 18 2008, 04:50 AM