Hello. Thanks for your updating. I think I am having a similar problem to you when I unplug my mkr1010 and power it with batteries. Actually I have this error:
processing.app.debug.RunnerException
at cc.arduino.packages.uploaders.SerialUploader.uploadUsingPreferences(SerialUploader.java:152)
at cc.arduino.UploaderUtils.upload(UploaderUtils.java:77)
at processing.app.SketchController.upload(SketchController.java:732)
at processing.app.SketchController.exportApplet(SketchController.java:703)
at processing.app.Editor$UploadHandler.run(Editor.java:2061)
at java.lang.Thread.run(Thread.java:748)
Caused by: processing.app.SerialException: Error touching serial port 'COM3'.
at processing.app.Serial.touchForCDCReset(Serial.java:107)
at cc.arduino.packages.uploaders.SerialUploader.uploadUsingPreferences(SerialUploader.java:136)
... 5 more
Caused by: jssc.SerialPortException: Port name - COM3; Method name - openPort(); Exception type - Port not found.
at jssc.SerialPort.openPort(SerialPort.java:167)
at processing.app.Serial.touchForCDCReset(Serial.java:101)
... 6 more
I am considering also to buy the regulator you are talking about. I would like to know if your Arduino showed also this input as an error before you fixed it with the regulator.
Thanks in advance 