I've programmed up a Atmel 328 processor with the bootloader and then uploaded example blink. Delays work normally 1sec.
When I use an Atmel 328 that doesn't have the bootloader programmed then the delays go from 1second to 15seconds (approx).
I used the blink.hex file from the Arduino build. When I use the Arduino to create the build I'm selecting the Uno board. So maybe I've selected the wrong processor when I'm using the avrdude to upload the file to flash?