I use studio 4.12.460 and elf files created with avr-gcc 3.4.1 in combination with a JTAG-ICE MK2 and a mega64.
Often I have to single-step (F11) several times (up to 15 on some lines) before Studio advances to the next line of code. The same happens with stepping-over (F10). I must mention that the response after every keypress is still quick and my disassembly window is NOT switched on.
I cannot think that this is a Studio bug because nobody else complained about it? Its been a while since I used debugwire, but as far as I can remember it didn't give me this problem.