Custom Arduino PCB - not working after assembly?

[CodeBreaker]

Hi guys!

I'm having a big issue with my design. Here's what happened.

I have made a custom Arduino PCB (Schematic and gerber files attached). I ordered Blank PCB and soldered it myself and it worked great. I rearranged the PCB and send it to production to be assembled. After receiving them I went on and programmed them. After successfully burning program using Arduino as ISP I went and checked the serial port and to my surprise, nothing was written there. So i burned a simple blink program and instead of blinking the output pin, the pin was always at 5V. So all the pins I set to pinMode(LED, OUTPUT); are always on HIGH regardless if the program sets it to HIGH or LOW. I don't understand the problem. I can burn the program to the ATmega328P with no problems but when using the outputs I always get 5V. The test PCB with the same components is working perfectly. I only rearranged the components and let the autorouter do its thing (No errors). I've checked continuity on all pins and they are correctly wired. I can also burn the bootloader and flash it with Arduino IDE as a regular Arduino. So, what gives?

Did i mess anything up with the rearranging of the components? is it possible that something happened in the assembly stage or transport?

I hope I don't have to toss $2000 in the trash...

[Sparker]

I don't know how they handle fuse bits in Arduino, but maybe you have to set them up properly on a new MCU. Some devices might have a watchdog timer running by default. 

[Yansi]

Is there any manufacturer's bootloader in that AVR, or does the arduino use a custom bootloader?

The voltage regulator has the input cap where?!

[CodeBreaker]

I love you man! And I'm an idiot. Thank you very much.

On the test board I burned Arduino bootloader first which set the fuse bits and on the new one I burned the program without setting the bits. 

[Sparker]

Cool! Once I also wasted some time because I forgot about the fuse bits... now it's fused in my brain to always check them.