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.