engine boots and v3

I am using net-snmp in an embedded platform.

Everything was working fine in v3 mode. Then the issue came where if the device was rebooted the engineboots was always 1 - which in turn caused MgSoft to reject all v3 packets from my device.

So I tried to fix this by keeping track of the engine boots in a sql table and calling 
engineBoots_conf("snmpEngineBoots", boots); with the updated value.
This did rectify the reboot issue with Mgsoft but now I no longer see traps. I tried removing the call I added and that does not rectify the situation as I think net-snmp has its own idea of what the engine boots should be based on what I told it from a previous load.

Any info on how engine boots should be handled would be greatly appreciated.
My engine id is constant.

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