Have you tried checking the fuses on your chip to make sure they match Arduino's default settings? If it was not an Arduino board to begin with, some products come with different configurations. This has caused us problems in the past. Be careful with setting fuses, you can flash configurations that "soft-brick" the chip, requiring high voltage programming to reverse. Some can be changed without issue.
The Atmel Studio debugger is not foolproof under any circumstances, but we've gotten it to work with Arduino with some degree of success. Hard to say what might be causing the problems you describe without more detail though.