I have no experience with any of the MKR boards (!!)
Boards with native USB have the glowing / pulsing as an indication that the boot loader is active. Double tapping the reset button should also show this. You can also simulate it by opening and closing the serial port with a baudrate of 1200 baud (e.g. using serial monitor).
However, the boot loader will only stay active for a few seconds so it does not quite make sense that it's the boot loader.
Please show your sketch. Any serial print / println statements in there?
Note that your topic has been moved to a more suitable location on the forum. Installation and Troubleshooting is not for problems with (nor for advise on) your project 
See About the IDE 1.x category.