I've made pcb with Atmel 328p, with external Xtal. Made also some before, with no problems.
Now I had problems with using serial lines, and as it seems cpu is NOT using external Xtal (16Mhz).
(made little test sketch with blinking output every 100ms, but blinking is much slower.)
Loading scetch using ISP, and arduino uno as programmer.
So Uno is loaded with software: ArduinoISP, IDE I've selected "Arduino as ISP"
And as board, I've selection pro/mini, 328p 5v-16Mhz.
So loading of the sketch seems ok. But running mode is whitout the Xtal (I think).
(However, "Burn bootloader" will also set the fuses to include "use external crystal", rather than the default "use internal clock." You can do that with avrdude directly, but "upload using ISP" does NOT do it.)