Yes I am, how was the bootloader set up?
I use an Atmel AVR ISP MKii. I use the IDE to burn the bootloader first to make the fuses are set correctly.
The times I forgot to that, I spend a frustrating 1/2 figuring what is going on, eventually figuring out the clock is really slow, and then finally remembering to do the bootloader for the fuses. Getting better about that.
I then use File: Upload Using Programmer with the MKii if I don't need the bootloader, or I connect up an FTDI Basic for downloading sketch via serial interface.
I don't use the Optiboot 16 MHz tho, I always use Bobuino so Serial is at D0/D1, SPI is D10-11-12-13, and I2C is A4/A5 of D18/D19, just like on a '328 board. I like a little consistency.