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

I am uploading sketches from Native USB port on Arduino IDE. I think that there is no distinction between native and programmer USB port on Arduino Create. Can this be a reason of problems? On programmers USB port I get errors

Build options changed, rebuilding all
Sketch uses 10120 bytes (3%) of program storage space. Maximum is 262144 bytes.
Open On-Chip Debugger 0.9.0-g932ec70 (2017-02-15-12:34)
Licensed under GNU GPL v2
For bug reports, read
	http://openocd.org/doc/doxygen/bugs.html
debug_level: 0
adapter speed: 500 kHz
adapter_nsrst_delay: 100
cortex_m reset_config sysresetreq
Error: unable to find CMSIS-DAP device
Error: No Valid JTAG Interface Configured.
Error: No Valid JTAG Interface Configured.