Why do you keep suggesting the problem is/may be PTP/MTP?
Is there any good reason to think that that is the problem? Considering, that the Kindle emphatically is not a PTP/MTP device....
...
Are you suggesting that Windows thinks it is an MTP device anyway? That would be kind of silly
but anyway, people have provided Debug Device Detection, and no erroneous PTP/MTP devices were listed by calibre either.