This patch was mentioned in this thread on the Earth & Beyond Forums, as a final solution for the dreaded 'Earth and Beyond is Already Running' error popup. The person who made the patch basically took the client.exe binary, and used a binary editor to make a 1 byte change to making the client skip the already-running check. I have downloaded it, check it against the original clint.exe, and put it here for posterity -- as the original uploaders site to download from appears to be down now.
I have used this binary patch for severa months and have never seen the Earth & Beyond is Already Running popup.
Download the binary patch zip file, unzip it, and do whatever due diligence you do to security check binaries randomly downloaded from the net -- virus scan, etc.
Once you feel it is safe to use, rename the 'client.exe' file in the release folder of your Earth & Beyond installation to something like 'client-original.exe'. Then copy the client-multiplayer-patch.exe file to the release folder and rename it to 'client.exe'. Then start up Earth & Beyond as normal.