I am having the same problem, I run a 80 player minecraft server. I do however have a SOLUTION that sometimes work but does not in all cases.
Go to the server properties file and make sure enable query is TRUE as this enables websites such as planet mine craft to ping the server and check if its online. However this did not work for me so i am doing a massive range of trouble shooting, as soon as i find out how to fix it i will post it here.
