It all depends on the implementation. Which SNMP counters are you talking about or for which purpose these counters are used.. The time interval differs for different counters. THis seems to be an issue with the clocking. Are you using internal source of clocking?? Or is it external source.
On Cisco devices, the counter update rate is typically 10 seconds.
1) What are the devices being used and what are their IOS versions?
2) What MIB objects are being polled and what are the values returned?
These details are very much necessary to find out what's really
going on and to decide if it's really a problem or not.Captures of
debugs on the box may also be helpful.