Hi,
We had problem with the above error message with our certificate when we moved to AnyConnect 3.1
We were instructed to request a new one
Also here is the link to Cisco site we were provided that explains the changes in 3.1
IPSec and SSL connections require server certificates to contain Key Usage attributes of Digital Signature and Key Encipherment, as well as an Enhanced Key Usage attribute of Server Authentication or IKE Intermediate. Note that IPSec server certificates not containing a Key Usage are considered invalid for all Key Usages, and similarly an IPSec server certificate not containing an Enhanced Key Usage is considered invalid for all Enhanced Key Usages.
Link to document
http://www.cisco.com/en/US/docs/security/vpn_client/anyconnect/anyconnect31/release/notes/anyconnect31rn.html#wp1049936
Sadly I dont dable with certificates myself so I'm not really familiar with this.
- Jouni