I am experiencing the same problem as you with one linux server (on other servers it works fine for me). I found that cookie management produces this problem but i didn't find the solution.
What happens: the IE client trying to connect to mambo but it can't estabilish an connection. Only after erasing cookies, IE client successfully connects to the mambo. During this time, who's online counter significately increases.
I find some other bugs related to the random logouts (user successfully login based on cookie, but if he try to click on any link it appears that he is no longer logged in). Funny, isn't it?
Do you use SoutIt module? I didn't check, but i found some errors within SoutIt module which appears to be cookie management - related (???)
The error message was:
Fatal error: Call to a member function getAroGroup() on a non-object
in mambo.php on line 187
All of these symptoms may have influence on wrong number of "Who's online" module.
I am using Mambo 1.0.9, u can see it at
http://www.studentskiforum.com