As long as the 2nd number, time spent on queries, is low then your MySQL server is running and handling the queries fine. Do you have SSH access to the server? If it's a unix box then when you notice the slow times you can run 'top' on the server and get an idea of what's going on at the server level. Maybe a high load average at the time, something of that nature.
I assume you're still running 6.5? I'd keep an eye if the slow times appear on any particular pages. From the looks of the debug line it just appears that for some reason the server has a lot going on at that particular time.
