Strange behaviour of arduino based board

Hi,

I have been developing for quite a while a arduino based board that as 2 ATmega 2560 and 1 ATmega328.

The system designed has been stripped of its FTDI programming component. I use an external FTDI breakout board to do the programming of the 3 processors. Each has a 4 pin plug (i modified the FTDI, shunted the 3V3, CTS and GND terminals, so i can save space and use only 4 pin programming).

Until now i had no special issues to register in terms of programming or program running but my latest versions are giving me problems. Now when the program runs, it´s like... getting delayed or even freeze. From what i have been able to test the problem is related with the serial programming interface.

The behaviour is the following:
If i have the FTDI plugged in to listen to whats happening everything runs smoothley;
If i start the board without it, i get the problems mentioned above.
Strangely from my hardware debug i have been able to understand that if i shunt either the TXD0 or the RXD0 or both with the GROUND when i start everything (without the FTDI plugged) goes OK.

This setup as been working for sometime, but since the last batch of orders i made this issue appeared and it seems a little bit random. The behavior doesn´t appear in all boards, but from the testing it is always solved by either plugging in the FTDI or shunting the TXD/RXD to the GND pin.

I have the feeling that it could be some issue with the TXD/RXD lines and the bootloader. Maybe the bootloader gets delayed or hangs because they are on the air, when i take out the FTDI or do not shunt these pins.

Does anyone have any suggestions. Or further testing ideas. Or did i do something wrong in the electronic design?
I´m really on a dead end here to understand whats happening...
Seems like that book about electronics called, "Black Magic"...

You can see the detail of the schematics i use for the programming of the MCUs: https://dl.dropboxusercontent.com/u/7216207/Schema%20Serial.png

The details of the FTDI connector modifications can be seen in the image:
https://dl.dropboxusercontent.com/u/7216207/FTDIJPG.JPG

The details of the PCB Board setup can be seen here:
https://dl.dropboxusercontent.com/u/7216207/Board.JPG