It shouldn’t be a problem to restart the SpamAssassin process, you should be able to do that as often as you like. It sounds like what you’re seeing may be another issue, though I’m not sure what at the moment.
You’re saying it works fine on the other server?
And just to clarify, what screen is it you’re going to where you see that error?
Lastly, if you look in System Settings -> Feature and Plugins, is the “Spam filtering” feature enabled?