Just did a fresh install of WordPress 3.1.3, added a StudioPress theme and acvitated Akismet 2.5.3.
I got the following error:
The plugin generated 176 characters of unexpected output during activation. If you notice “headers already sent” messages, problems with syndication feeds or other issues, try deactivating or removing this plugin.
I deactivated and then reactivated and got the same error.
Have you tried grabbing a fresh copy of the Akismet plugin to make sure the one you have hasn’t been altered in any way? If the regular Akismet 2.5.3 plugin was doing this I would have expected millions of complaints by now.