It can be tricky, because php can eat up just as much as mySQL if you let it. Ussally you associate more load with alot of mySQL queries because of the disk access going on. But php can cause just as much load checking and changing data for output.
Are you in a shared hosting enviroment? Other sites on the box can cause extra load server wide, remember you are all sharing the same resources.
What I would do is enter de-bug mode, and see if a mySQL query is taking awhile to run, if not you know you have a problem with some slow php code.
BTW you have defentaly increased the number of queries on index.php, I belive the stock installation runs 7 without vBcron, and 8 when vBcron is invoked.
This is vB3 we are talking about right?