Hey manly,
The SM server does a load of custom security checks, where it works out an MD5 hash (a mathematical calaculation based on the contents of a file) on the bf2 core files to see if any have been tinkered with or dodgy hack files added.
These MD5 checks have been around since the first week of the SM server going online, so it's not any new updates that have caused it.
Computers are expected to respond to 1 check every few minutes (so it shouldn't cause any additional lag) - if a computer doesn't respond for a long time the server may kick them for 'ignoring md5 tool queries'
The usual cause of this is dodgy internet connection, bf2 just fucking up.
Usuall it's dodgy internet. If the problem keeps occurring then it might be something else, but let us know