This is a problem with the folding client. Not so much a problem really but it's a matter of the idle priority. The priority for the Folding client is set at a lower idle priority than the seti client.
This was the situation when it started then they upped it to a higher idle priority(4?) for a short while and that allowed it to work side by side with seti, but it is back down to idle 1 I think. To make matters worse this priority was set in a sub thread that is responisble for all the work and even when you try to change to priority in the windows task manager it wouldn't change.
I am not 100% sure that this is what happened, but it's been a problem in the past. I thought it went away but it appears that it hasn't.