For what it's worth, I took a book we had recently published, "Write like the Wind, Volume 1" by Aaron Paul Lazar, which had the following properties:
1) was converted to mobi from epub via Kindlegen 2.5 (command line program on Linux);
2) the mobi file produced by kindlegen appeared fine on all "devices" in the kindle previewer;
3) when the file was side-loaded to a Kindle 3 with firmware 3.4 (i.e. KF8) it exhibited the problem with opening in the wrong place.
4) the file was uploaded to KDP, and after it went live I purchased it over the air from the same Kindle 3. The purchased file opens correctly (to the "Introduction" chapter).
So, at least in the case of the Kindle 3, Amazon does seem to "fix" the file before download.
Edited to add, the purchased book is supposed to be DRM free, in case that should matter as to the fixing of the problem.
BTW, the book is priced at $0.99, so it shouldn't "break the bank" of anyone who wants to experiment with it on other devices.
(And no, this isn't a cheezy attempt to sell books -- it's for Science!)