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You mean that the STK500 v2 programmer uses an emulated serial port rather than direct USB? Then I guess there is a bug in the Arduino IDE. The file programmers.txt contains the following lines describing the programmer:

avrispmkii.name=AVRISP mkII
avrispmkii.communication=usb
avrispmkii.protocol=stk500v2
avrispmkii.program.protocol=stk500v2
avrispmkii.program.tool=avrdude
avrispmkii.program.extra_params=-Pusb

You may locate this file in your Arduino installation and replace the last line from this snippet by

avrispmkii.program.extra_params=-P{serial.port}

If that works, it would be a good idea to submit a pull request with the fix to the Arduino team.

Alternatively, you may try selecting "Atmel STK500 development board" as a programmer. This is supposed to autodetect the version of the STK500 protocol, and uses the correct serial port.

You mean that the STK500 v2 programmer uses an emulated serial port rather than direct USB? Then I guess there is a bug in the Arduino IDE. The file programmers.txt contains the following lines describing the programmer:

avrispmkii.name=AVRISP mkII
avrispmkii.communication=usb
avrispmkii.protocol=stk500v2
avrispmkii.program.protocol=stk500v2
avrispmkii.program.tool=avrdude
avrispmkii.program.extra_params=-Pusb

You may locate this file in your Arduino installation and replace the last line from this snippet by

avrispmkii.program.extra_params=-P{serial.port}

If that works, it would be a good idea to submit a pull request with the fix to the Arduino team.

Alternatively, you may try selecting "Atmel STK500 development board" as a programmer. This is supposed to autodetect the version of the STK500 protocol, and uses the correct serial port.

Edit: you may also have to replace

avrispmkii.communication=usb

by

avrispmkii.communication=serial

C.f. this bug report , which seems to cover the exact issue you are facing.