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
In the past I have sometimes found that switching off compiler optimisations can solve 'missing' breakpoints, as the optimiser had determined (correctly) that the code was not being called, and removed them from the compiled versions.
This does sound like a different issue, but it might be worth making sure that optimisation is switched off in Debug mode. [Project / Properties, Build settings tab]