My main comment is that by wiring the output of the dc/dc converter directly to the arduino's 5vdc bus and then plugging in the usb cable you are 'hard-wiring' two different +5vdc voltage sources together from two different regulators. This is never considered a good engineering practice, although many do so anyway, often with no problems reported. Note that the arduino board uses a mosfet to isolate the on-board +5vdc regulator's output voltage from the USB +5vdc voltage, and thought that was important enough to add that isolation circuitry.
I suspect your dc/dc converter doesn't play well with another +5vdc voltage source wired to it's output. Now as to why the serial converter chip is more sensitive to whatever fault condition it's being subjected to, I don't have a clue. But I have no doubt that the root cause is based on the hard-wiring of two independent and active voltage sources being wired together.
As the song says, sometimes you are the windshield, sometimes your the bug.
Lefty