If the estimate displayed on the site stays too low for more than 15 minutes, then you are almost certainly experiencing hardware errors.
cgminer checks every solution generated by your GPU, and if one turns out to be incorrect because of hardware errors it (rightfully) doesn't even submit it. Since pools can only estimate your hash rate based on how many solutions you submit in a given amount of time, their estimate will be lower than your real raw hashrate. This raw hashrate, which is correctly displayed by cgminer, is, however, not meaningful if the solutions your card generates are wrong.
You need to make sure that all (not just the top one) of the HW figures in cgminer are zero or next-to-zero; if that's not the case, you need to review your settings. Make sure you carefully read the documentation about scrypt mining provided with cgminer.