Arduino USB Serial Communications stops working after uploading sketch.

I use arduino Mega 2560s on 3d printers. I have uploaded code many times, made changes, uploaded again until everything is working correctly on the 3d printer. I was recently forced to change computers doing the uploading and am now running a newer version IDE. I don't know the older version but I am now running 1.6.13. When I upload the marlin 3d printer firmware the first time everything works perfect. If i try to upload it again I get a timeout communicating with the board. I have done the loop back test and it fails. The receive light blinks on the board but nothing is returned. The loaded sketch does return serial data to the computer every time I hit the reset button on the arduino. This means the arduino can transmit but something is wrong in the receive end. I played around with the 16u2 chip doing the usb serial communication and what I found with an oscilloscope is the receive data is a good digital signal at pin 9 of the 16u2 chip. It then goes into a 1k resistor and connects to PE0 on the Atmel mega 2560. The signal at the 2560 is the correct digital signal, hovever it is not getting low. The low is around 4 volts and the high around 5 volts. The input to the resistor shows a low of 0 volts. I have checked the resistor and it is 1 k like it should be. It seems to me that somehow the RX data input, PE0, is somehow loading or pulling up the signal. There is nothing else connected to this pin. I don't see anyway with the serial commands in the sketch to determine if there is any type of load or pullup on this pin. This has happened to 3 mega 2560 boards so it is not a one time failure. Where can I look or what can I check to determine if there is a pullup on PE0?

The newest version of the IDE is 1.8.5

My guess is the board isn't getting reset - is the shield holding the reset line high or something? Does it have something connected to the serial lines?

I'll bet with the shield removed it would work.

I am testing with the shield removed so there is nothing connected to the serial lines. I know the reset is working because every time I press it the board sends serial data to the computer. Is their a reason to switch to IDE 1.8.5?