No, it doesn't matter how frequently you check your email, but the time before your email program decides the server is inactive and shows the time out message. It is in your email programs settings, this is an example of OE's time out setting:
Find the equvilent in your email program and increase it.
There have been changes to the latest versions in the Internet Mail provider which may have had an impact on your email scanning (this is what is going on when the email program thinks the server is idle).