I had the same issue - the way I solved it was that I was using the wrong firmware for the R4 card that I bought.

The link here goes to the firmware for the BASIC R4 card. I bought the R4-SDHC card (full name R4i-SDHC or something like that) with WiFi. You have to get the CORRECT firmware to use the card you have.

My R4-SDHC card actually had the website printed right on it. It is www.r4i-sdhc.com. There, I downloaded THEIR firmware for the card they manufactured. You extract the file and put it in the ROOT (lowest) directory of your R4 card. It should have 4 files/folders (mine did anyways). Mine had 3 folders called:
- moonmemo
- moonshl2
- R4iMenu
and a file called:
- R4.dat

I put those in the root directory - manually created a Games folder in the root as well and dropped my extracted (will have a .nds filename) games into the Games folder... started it up and voila!

Make sure you tap GAMES to get it to run, not the bouncy ball - you'll get a WiFi error if you haven't configured it yet.

Hope that helps.