CPU time is allocated in two ways - user and system. Think of system time as the cpu necessary to provide service for the user's cpu needs. Waiting for disk/memory/network, swapping processes in and out, all of these shouldn't be billed to the user as part of their CPU allocation.
Now, why you got a zero is probably due to not having any data for the period. But it can also occur if you used so little CPU that as a percentage of the entire CPU available, you didn't use much.
Note also that cpu accounting is done on a per user basis so your web site may be using a different user and the cpu stats are stored under that account.
Check 'em all. It should make reasonable sense then.