Programs disappear from the brain when uploaded from RobotC in the teleoperated mode. When RobotC is switched to the autonomous mode, the programs stay, but appear in the autonomous menu, which turns off the connection to the remote controller. So, you have to stop the program, get out of the autonomous menu, go into the teleop menu, wait for the controller to connect, then select the program and start it.

Which version of ROBOTC for VEX Robotics 4.0 is being used (this can be found under the 'Help -> About ROBOTC' menu option)? There were a couple of issues in 4.05 and prior that are fixed in 4.06, you can find more information on these issues (such as programs not appearing in the correct list on the IQ brain) here:http://www.vexiqforum.com/forum/main-category/technical-discussion/556-is-there-a-way-to-test-flash-memory-on-cpu

You can also upgrade to the 4.06 version of ROBOTC for VEX Robotics by navigating to the 'Help -> Check for Updates' option in ROBOTC, or you can manually download and install the update here: http://www.robotc.net/download/vexrobotics/

If updating does not solve the issue, please send in a support ticket to support@robotc.net and we will be more than happy to assist you with this issue.