I use CKS devtools version 1.1(latest).
Problem is: I installed tools and everything was ok relating to debug (VS2010 - Tools - CKSDEV -Attach to IIS Worker Processes) but after I changed deployment of my custom SP site template to another web application CKSDEV tools won't do debugging anymore. When I click on above link tools become "connected" to IIS wprocesses (everything seems ok), but I can't get inside of my breakpoints.
p.s. everything was deployed and activated ok, i did IIS resets, PC restarting, redefining place of breakpoints but that didn't helped. Also my collegue experience same problem on his pc after he changed web application and site collection path.