I have an iMac 21.5" (late November 2010, OS X 10.6.8 with latest updates). I bought a wireless keyboard and mouse at same time. When I started up with ⇧ shift or ⌥ alt/option key down, the computer starts up from the internal drive. No SafeBoot or Startup options.
When I attached a USB keyboard and mouse and started up with the ⌥ alt/option key down, I was able to choose between the internal drive and backups on external drive. The wireless mouse was inactive at this time. When I selected a drive with the USB mouse, it asked me for a password. From that point forward, everything worked normally. The wireless mouse works to move the cursor to the text box and the wireless keyboard works to enter the password.
I replaced batteries in keyboard and mouse, installed OS X 10.7 Lion, reset NVRAM using USB keyboard - Still same issue.
The green light on keyboard comes on momentarily during startup, so the iMac must be communicating with the keyboard. After that, the light goes off and can be turned back on for a few seconds by pressing switch on right side of keyboard. By doing this repeatedly during startup as soon as the light went off, I got the startup options once.
I checked System Preferences → Bluetooth → Advanced. The first 3 checkboxes are checked. The 1st checkbox is "Open Bluetooth Setup Assistant at startup if no keyboard is detected". I never understood this, I assume it indicates that the keyboard is detected. The iMac can be awakened from sleep with keyboard and mouse.