Serial tower RCX 1.0 works with NQC but flakey with RIS 2.0
What a strange issue. I'm not sure the exact cause, but I have a few troubleshooting tips for you to try:


Make sure the serial tower is set to "Long Range" mode (the little switch on the front).  
Make sure the RCX is set to "Long Range" mode (Go to the RIS settings page and change the RCX comm range).
Make sure the RCX program slots are unlocked (also in the RIS settings page).
Try replacing the batteries (again, particularly in the tower).  
Try downloading the program with the lights off (believe it or not, I've had lightbulbs emitting enough infrared to interfere with communications).
Make sure that when the RIS software is running, no other mindstorms software is running. If NQC is running at the same time it might bind up the serial port.