First, thanks for the reply, but I don't think that answer will solve the problem I'm having.
The problem is not a timing issue, its that the first batch file is located on the thumbdrive, and it copies a couple batch files to the local machine, and starts to execute the second one. The idea is at this point, i should be able to remove my thumbdrive, because all the files that it needs have already been copied to the local machine, and the one batch file that is on the thumbdrive has already executed all of its commands, and passed control over to the second one.
When I remove the thumbdrive, however, the batch files ends when I close the .exe file, and does not execute the final command of "restart the computer". If I leave the thumbdrive in, everything works flawlessly, so i believe the problem is with the final command in the first batch file utilizing START. Either I'm using the wrong command, or not utilizing the correct arguments to truly pass control to the second batch file.
Maybe I'm not explaining things properly... let me briefly recap.
I've got a folder named "customizer" on my thumbdrive that contains a customizer.exe file. In the root directory of my thumbdrive, I have a batch file that copies the entire contents of the customizer directory to the desktop of the local machine, then run a second batch file located inside the customizer folder. This second batch file runs the customizer.exe file, waits for the user to close the program, and then restart the computer. On restart, the computer executes a 3rd batch file located in the all users\start menu\startup folder that deletes the customizer folder on the desktop and then deletes itself from the startup folder.
Everything works flawlessly if I leave my thumbdrive in the computer, but currently it will fail if I remove the thumbdrive. I only remove the drive after the .exe file has been started, because I know the files are done copying at that point. I believe the problem is that the first batch file is not fully ending and then starting a new process for the second batch file. This would explain why everything works flawlessly when the thumbdrive is in, but stops executing commands when it is removed, taking the first batchfile with it.