I am configuring an IDSM2 module in a cat6500 siwtch running CatOS. I configured some VACLs to capture traffic to send it to the data port of the IDSM2 but I started to have connectivity issues with the vlans I mapped to the VACLs. As far as I know the VACLs with the capture option do not block or affect the traffic flow, is this correct?
Yes, but the VACL has implicit "deny any" at the end, so you'd use:
set security acl acl-name permit ip any any
otherwise all other traffic will be blocked.