I'd be curious why the rediscovery is overwriting your custom interface speed. I do not think it is supposed to do that. If the rediscovery is supposed to overwrite your custom speeds, what is the point of custom interface speeds if they never stay custom?
I haven't addressed that yet, but I agree. However, my immediate concern is getting net-snmp to report the correct ifSpeed, so it doesn't get overwritten.
Incidentally, I'm on V10 SP1...
We have also seen this on older versions of net-snmp (5.1.X on Debian etch) and custom interface speed has worked correctly (NPM10 SP1)
Net-snmp (126.96.36.199 on RHEL) reports correctly for us, I would suggest opening a support ticket on the rediscovery issue.