I think this should be fixed in 1.2.6. Let me know if it isn’t.
In my case the new version 1.2.6 did not fix the correct com port detection.
Unfortunately I’m having the same issue. Win 10, Alchitry IDE 1.2.6 or loader both fail to flash. Followed full IDE installation, and win 10 ISE tricks too. Also manually selected the Mojo V3 driver in device driver.
I just pushed 1.2.7 which should fix the Mojo issues. I was able to replicate the original issues with a clean Windows 10 install and this should hopefully get it all working now.
Yes problem solved. 
I did some tests with both Alchitry-Loader and Alchitry-Labs 1.2.7
and the port is detected correctly if the mojo driver is (Mojo V3) with the native windows 10 serial driver the Mojo is not detected.
Thank you
On this same topic:
I have Mojo V3 Loader installed, but have misplaced the USB driver (inf file)
Is there someplace on this site I can download the driver? (Win 8.1 64 bit OS)
Searched quite a bit and came up empty.
Thanks,
Mike
SUCCESS
I installed Zadig driver tool (search and download for free) and the Mojo V3 showed up in the USB device list.
Used the USB Serial (CDC) driver (takes a bit to install) and then Mojo V3 appears as a new COM port.
Driver is Windows\system32\DRIVERS\usbser.sys in the device manager properties for the COM port.
Mojo V3 Loader works with this COM port.
Hope this helps others.