I have seen twice that my newly found 8-chains share not showing in "share value" display on the upper right of the ypool's page. Both times the display responded to 6-chains and 7-chains like clockwork. So it was not a problem with network or pool's down time. The XPM column in the personal stat page didn't have any change more than 0.001 after the above 8-chains were found. Not all 8-chains are missing. Often they do get counted. (Because my 8-chain/h is less than 1, most times it is the 6-chain/7-chains that contribute to the XPM column. So once an 8-chain is found you can see the result in the XPM column, if it gets counted.)
I am wondering what was happening. I am using one of the unofficial miners. Is it possible that the miner is secretly sending some of the more valuabe shares to another account?
More than likely what is happening (and you can verify this by keeping an eye on your miner's output) is that those shares end up invalid for some reason. Most often (for me) the cause of this is finding a share right as a block is solved, causing the share to become outdated.