I have experienced the same issues.
The compiler warnings seemed to be associated with the latest boards update (.13), but they do not always show up for me. Sometimes they do and sometimes they do not.
Debugging seems to leave a lot of extraneous files in my sketch directory and I think that old versions of these files might be causing instability in the debug process.
I have found that if I copy the code of an existing sketch into a new sketch and then debug the new sketch then that yields more a more reliable debugging process.