I am running Visual Studio 2008 with SP1. When I debug an application, it will skip over my break points.
For example, I have two lines of code, each call a method.
It's possible that your symbol file (.pdb) is out of sync with your source code. A common symptom of this is:
When debugging, you should never see the debugging pointer stop on a blank line, and this would indicate that you have a symbol/source mismatch somewhere.
This sort of mismatch could also cause breakpoints to be skipped like you are seeing, but cleaning the solution generally fixes it (and it sounds like you have tried this already).
The other option (as suggested by others) is that you aren't building a Debug configuration. While it is possible to debug a Release build, the code is significantly optimised which can make the debugger act strangely, e.g.
One other important thing to note is that breakpoints cannot be set on every line of code. For example, if your code only has a variable initialisation:
long numObjects;
the breakpoint will generally not be set properly (although it will usually move to the next line of "real" code). However, if your line of code initialises the variable:
long numObjects = 5;
the breakpoint can be set.