Unfortunately you can't disable just one of the Discovery Protocol Tables.
How to Discover and Model the Network - CA Spectrum - 10.2 to 10.2.2 - CA Technologies Documentation
Discovery Protocol Tables (enabled by default) - Determines whether Discovery uses the Discovery Protocol tables when mapping device connectivity. Supported discovery protocols include Cisco, Nortel, Cabletron Switch, Extreme, Alcatel, Foundry, and Link Layer.
To further troubleshoot this, enable the "Debug AutoDiscovery" (to On) in the "AutoDiscovery Control" subview of VNM model. Then try to discover connections (select one of the model, right-click, select Reconfiguration --> Discover Connections). Once the discover connection action has finished, disable the AutoDiscovery debug mode.
Review the $SSPECROOT/SS/ADiscDebug_yymmdd_hhmmss file.
If you need further assistance, please open a case at CA Technical Support, attach the ADiscDebug_yymmdd_hhmmss file, $SPECROOT/Install-Tools/.history file, sapwalk2 output of the 2 Cisco devices (the sapwalk2 utility is located in $SPECROOT/bin/ directory) and the connection information (i.e.: Cisco1-Port_25 <--> Port_14-Cisco2).
sapwalk2 syntax:
sapwalk2.exe -i <IP_Address> -v v2c -s 1 -c <community> -o device_name.walk
Thanks,
Silvio