Arduino MKR ZERO blink sketch only works when uploaded from online editor

Hardware MKR Family MKRZero
7 
Sketch uses 10120 bytes (3%) of program storage space. Maximum is 262144 bytes.
Forcing reset using 1200bps open/close on port COM4
PORTS {COM1, COM4, } / {COM1, COM4, } => {}
PORTS {COM1, COM4, } / {COM1, COM4, } => {}
PORTS {COM1, COM4, } / {COM1, COM4, } => {}
PORTS {COM1, COM4, } / {COM1, COM4, } => {}
PORTS {COM1, COM4, } / {COM1, COM4, } => {}
PORTS {COM1, COM4, } / {COM1, COM4, } => {}
PORTS {COM1, COM4, } / {COM1, COM4, } => {}
PORTS {COM1, COM4, } / {COM1, COM4, } => {}
PORTS {COM1, COM4, } / {COM1, COM4, } => {}
PORTS {COM1, COM4, } / {COM1, COM4, } => {}
PORTS {COM1, COM4, } / {COM1, COM4, } => {}
PORTS {COM1, COM4, } / {COM1, COM4, } => {}
PORTS {COM1, COM4, } / {COM1, COM4, } => {}
PORTS {COM1, COM4, } / {COM1, COM4, } => {}
PORTS {COM1, COM4, } / {COM1, COM4, } => {}
PORTS {COM1, COM4, } / {COM1, COM4, } => {}
PORTS {COM1, COM4, } / {COM1, COM4, } => {}
PORTS {COM1, COM4, } / {COM1, COM4, } => {}
PORTS {COM1, COM4, } / {COM1, COM4, } => {}
PORTS {COM1, COM4, } / {COM1, COM4, } => {}
Uploading using selected port: COM4
C:\Users\macie\AppData\Local\Arduino15\packages\arduino\tools\bossac\1.7.0/bossac.exe -i -d --port=COM4 -U true -i -e -w -v C:\Users\macie\AppData\Local\Temp\arduino_build_213938/Blink.ino.bin -R 
Set binary mode
readWord(addr=0)=0x20007ffc
readWord(addr=0xe000ed00)=0x410cc601
readWord(addr=0x41002018)=0x10010305
version()=v2.0 [Arduino:XYZ] Oct 20 2016 15:20:47
chipId=0x10010005
Connected at 921600 baud
readWord(addr=0)=0x20007ffc
readWord(addr=0xe000ed00)=0x410cc601
readWord(addr=0x41002018)=0x10010305
Atmel SMART device 0x10010005 found
write(addr=0x20004000,size=0x34)
writeWord(addr=0x20004030,value=0x10)
writeWord(addr=0x20004020,value=0x20008000)
Device       : ATSAMD21G18A
readWord(addr=0)=0x20007ffc
readWord(addr=0xe000ed00)=0x410cc601
readWord(addr=0x41002018)=0x10010305
Chip ID      : 10010005
version()=v2.0 [Arduino:XYZ] Oct 20 2016 15:20:47
Version      : v2.0 [Arduino:XYZ] Oct 20 2016 15:20:47
Address      : 8192
Pages        : 3968
Page Size    : 64 bytes
Total Size   : 248KB
Planes       : 1
Lock Regions : 16
Locked       : readWord(addr=0x41004020)=0xffff
readWord(addr=0x41004020)=0xffff
readWord(addr=0x41004020)=0xffff
readWord(addr=0x41004020)=0xffff
readWord(addr=0x41004020)=0xffff
readWord(addr=0x41004020)=0xffff
readWord(addr=0x41004020)=0xffff
readWord(addr=0x41004020)=0xffff
readWord(addr=0x41004020)=0xffff
readWord(addr=0x41004020)=0xffff
readWord(addr=0x41004020)=0xffff
readWord(addr=0x41004020)=0xffff
readWord(addr=0x41004020)=0xffff
readWord(addr=0x41004020)=0xffff
readWord(addr=0x41004020)=0xffff
readWord(addr=0x41004020)=0xffff
none
readWord(addr=0x41004018)=0
Security     : false
Boot Flash   : true
readWord(addr=0x40000834)=0x7000a
BOD          : true
readWord(addr=0x40000834)=0x7000a
BOR          : true
Arduino      : FAST_CHIP_ERASE
Arduino      : FAST_MULTI_PAGE_WRITE
Arduino      : CAN_CHECKSUM_MEMORY_BUFFER
Erase flash
chipErase(addr=0x2000)
done in 0.605 seconds

Write 10376 bytes to flash (163 pages)
write(addr=0x20005000,size=0x1000)
writeBuffer(scr_addr=0x20005000, dst_addr=0x2000, size=0x1000)

[===========                   ] 39% (64/163 pages)write(addr=0x20005000,size=0x1000)
writeBuffer(scr_addr=0x20005000, dst_addr=0x3000, size=0x1000)

[=======================       ] 78% (128/163 pages)write(addr=0x20005000,size=0x8c0)
writeBuffer(scr_addr=0x20005000, dst_addr=0x4000, size=0x8c0)

[==============================] 100% (163/163 pages)
done in 0.064 seconds

Verify 10376 bytes of flash with checksum.
checksumBuffer(start_addr=0x2000, size=0x1000) = 24fb
checksumBuffer(start_addr=0x3000, size=0x1000) = 2fd9
checksumBuffer(start_addr=0x4000, size=0x888) = 6c6a
Verify successful
done in 0.009 seconds
CPU reset.
readWord(addr=0)=0x20007ffc
readWord(addr=0xe000ed00)=0x410cc601
readWord(addr=0x41002018)=0x10010305
writeWord(addr=0xe000ed0c,value=0x5fa0004)