Hi there.
Thanks for reading my post, So I have created a schematic and have produced a few boards for testing, in terms of what it does it uses a 9DoF chip and an atmega chip to provide information about position/rotation.

So I had an issue with the first one where the atmega chip did not respond to anything when programming it with bootloader, I then got a second one created and I still have the same issue.
The atmega chip is not responding and checking the clock signal there is nothing at all, I check the usb-serial IC and that has a clock signal, but nothing on the atmega.

I am not sure if I have missed anything, but looking at this schematic, I have checked the documents for that IC and everything seems to be connected correctly also I have followed other designed that use the atmega to make there own arduino device

 

the usual suspect:

1) check the chip orientation;
2) check the pcb pin out vs. datasheet;
3) make sure that all the ground pins are indeed connected to ground;
4) make sure that the Vcc pins have the right voltage on.
5) make sure that the reset pin is at the right logic level.

The oscillator pins are not important for now - the default fuse should be to use the internal oscillator (if it has one).

After all of that, if it still doesn't work, it is interesting.

 

1) check the chip orientation;
2) check the pcb pin out vs. datasheet;
3) make sure that all the ground pins are indeed connected to ground;
4) make sure that the Vcc pins have the right voltage on.
5) make sure that the reset pin is at the right logic level.

1): Correct orientation.
2): Will have 2 check all pin layouts.
3): Looks like they all are
4): Voltages look ok
5): Cap to ground with 10k to High (should mean its held high?)

Thanks for the information. on further checking the board I am not sure what is wrong but I have noticed that areas of the Gnd plan have a higher voltage, when I checked Via on the Top right of the board and when referencing from gnd pin of the usb it shows as 3.0v difference.
Also on checking the two diodes on the usb input I have noticed D2 (closest gnd ref) is correct, but the gnd point on D1 is also 3v.
can you see anywhere that could be causing the voltage leek?
I have also made a change to the 3.3v regulator as it should have been feeding from the 5v not the vcc. but that doesnt affect it.
Here are the two main lines, gnd and 5v. Im going to check all the datasheets again, but if anyone sees an error please let me know.

 

Update:
I found that the Gnd on the usb was not connected to the gnd plane of the device so I have soldered a cable to link it to a gnd via. still doing testing