The maintenance task to remove vulnerabilities after 90 days only applies to remediated vulnerabilities. My best guess would be that you no longer scan for these vulnerabilities or have chosen not to remediate them. We do not remove vulnerabilities once they are discovered...unless they have been found 'not vulnerable'.
If you are using ticketing you can set the ticket to ignored so that the vulnerability will not show in scan reports. Another option would be to delete the asset from the Manage -> Assets screen and re-scan the asset with only the vulnerabilities that you wish to report on moving forward.
If the above assumptions are not the case...please feel free to clarify.
Thanks for your reply. I don;t believe that I am no longer scanning for a particular vulnerability but suspect what has happened is this :-
Scan A was set up with a range R1-R3
Scan B was set up with an OVerlap R2-R3 with different settings.
Scan B has now been deleted so will never clear the vulnerability, Scan A is still running and not showing up the vulnerabilities (but I think is still scanning for them).
Using the ticket system isn't really an option as from what I understand it doesn't stop the vulnerabilities from being reported in Custom Reports?
To give you an idea of size of my problem - I have nearly 1000 Assets with 28,000 stale vulnerabilities on them.
I have raised an SR for this but it does seem to be a bit of a limitation in the product.