PPS per second is really dependent on the model of switch. Cisco determines maximum packets per second based on 64 byte packets so it can be a bit misleading.
What I would look for:
1. Check CPU on swicthes / routers
2. Perform trace routes to / from different VLANs to determine avg latency
3. From wireshark, look for retransmisisons to check for dropped packets.
4. Avg Utilization
5. Avg packet size
6. check uplinks for dropped / discarded packets, crc, alignment errors (duplex mismatch)
7. Is there one particular host on the vlan sending bulk of traffic
8. Virus conditions - dos, syn, smurf attacks
You cna download filters from wireshark to check for these conditions.
9. is there a particular time of day this occurs? backups being done during business hours
10. any changes to the network recently? when did the problem start occurring?