After upgrading my system to kUbuntu 13.04 Raring Ringtail the delays in my avr-gcc compiled binaries had been gone.
After reading the #include <util/delay.h> documentation my eyes cached the __DELAY_BACKWARD_COMPATIBLE__ macro. After defining it the delays are working.

Workaround:

#define F_CPU 16000000UL
#define __DELAY_BACKWARD_COMPATIBLE__
#include <util/delay.h>
#include <avr/io.h>

int main(void
{
DDRB = 0xFF;
while (1) {
PORTB = ~PORTB;
_delay_ms(1000);
}
}



Currently I have a project which is based on the Atmel's NGW100 board.
It contains an 7' LCD display with touchscreen, an AC97 soundcard, a GPRS modem, and a PIC based board for controlling relay's, and so on.
The development time to make it working should be as sort as is possible. Read more...