Hi, I’m fairly new to working with XEM3010 and ran into a problem. 
I generated the counters.bit file by following the exact procedure given in the readme.txt and tried to program it through Frontpanel. It says “FPGA configuration complete” but the little gray box at the right end doesnt turn into color. Could you please help me out here :o
Make sure you properly added the UCF file (constraints) to your project. Without this, the pins will be mapped as XST sees fit and they won’t align to the proper pins of the FPGA.
You can also check your pad report to see where pins were mapped.