Can you please share your project which is failing?
I think the problem is related to the Miniprog3 that I was using; I switched to a different Miniprog3 and the issue seems to have disappeared. I will have to look into it more, but it seems like I might have damaged the programmer's functionality in some way.
Sorry for not posting this information earlier :(
Change the USB cable to a shorter one. That has helped some users.