Atmel Studio 6.1 has a new
RunOutputFileVerifyTask task that fails the build when the binary exceeds memory limit of the target board. This is a very useful check but can be a pain on certain occasions. It is fairly easy to disable though. Edit the
Compiler.targets file under [Atmel Studio 6.1 install folder]\vs and comment all elements where
RunOutputFileVerifyTask appears, including
UsingTask at the beginning.