Not sure about this error, but FYI... you should be using the newer LD9 installation media that has SP2 already slipstreamed into it, that has the "AMP" free installation. Then from there you install SP3.
Gotta agree with Spike. I just re-built my CORE from scratch last year when it caved. We loaded the SP2 release that has NO AMP in it and then upgraded to SP3. I was told, at the time of the reload, that certain elements which I would require would NOT be in the SP3 portion of the program if I did not load SP2 first. This Database version issue is likely a problem where the DB cannot properly upgrade from SP1 to SP3 without converting to SP2. The DB will indeed run an upgrade of its own at every SP / release change. So, given that you went from SP1 to SP3 I would:
1) Recover the DB to SP1
2) Recover the CORE to SP 1
3) Download the SP2 Build that Monsignor Spike mentioned.
4) Upgrade your core to the SP2 Release
5) Confirm that your security changed from AMP properly (a number of people had a problem with that)
6) Backup everything again (Core and DB)
7) Download the full SP3 release
8) Upgrade to SP3 as before
9) Confirm that everything is working
Before going anywhere or doing anything else go here to http://community.landesk.com/support/docs/DOC-23850 (the Core Install / Upgrade Landing Page). Despite it's name suggesting otherwise this is what I used as a guide to reload my 9.0 core when it became a smoking hole.
It sounds like your core and your console are not on the same patch level. Likely the latest service pack hasn't been applied to either the core or the console.