I've made several PCBs before using the SMD version Atmega 168/328 chips and not had any issues. But I changed the crystal in my most recent design because I needed something smaller.
I'm running the test at 5v with 16mhz, although I successfully tested the same design on breadboard running 3.7v at 16mhz with a thruhole crystal.
I thought it would be trival to substitute a thru-hole 16mhz 18pf crystal with this SMD variant:
My PCB didn't have room for USB connections, so what I did was put in the ISP header, upload the sketch to a working Arduino variant with the same Atmega328P, and read the flash contents with my MKII from the working board and write it to my PCB. All that works fine. But I can't get the sketch to run on the new PCB for the life of me.
I set my fuses as follows: Extended 0xFD, High 0xDA, Low 0xFF. The crystal seems to oscillate at 16mhz, but basically only between Gnd and 1V. If I change to use ExtFSCrystal at max settings, the crystal oscillates at 16mhz between about 1.25v and 3.75v. In neither situation will my sketch run properly (even putting a simple sketch like blink and scoping the output pin doesn't work).