Been running into this problem lately... When debugging an app in VS.Net 2005, breakpoints are not connected. Error indicates that the compiled code is not the same as the running version and therefore there's a mismatch that causes the breakpoint to be disconnected.
Cleaned solution of all bin file and re-compile doesn't help. Not just happening on a single box or person either.
Added Note: This solution is in TFS for Source Control. If I delete my local TFS repository and get it from source control from scratch, SOMETIMES the problem goes away. I've also tried un-installing and re-installed Visual Studio. That also SOMETIMES helps. That fact that both of those work some of the time indicates that the problem isn't caused by either directly.