It's all about the naming scheme for the files you're using. Typically, Audiobooks are broken down into Parts first and foremost and so Audiobook Builder's probably lumping all of your Part 1's together, all the Part 2's together, and so on because in many situations, this would be correct for an Audiobook where matching Part #'s go together. We'll have to look into factoring in this differing sort of situation—wherein a story is broken down into Chapters and then those Chapters broken down even further into Parts—when resorting dragged-in items.

Your workaround for adding the files three-at-a-time is certainly a good way to drag in the files, keeping them in order. Or, for a slightly quicker method for adding everything all at once, select all the files where they show in iTunes and use Audiobook Builder's 'Add iTunes' button. This should respect the way the files are intended to be ordered.

As for the Start time changes, we'll have to look into adding that sort of support to a future release. That's something that iTunes saves, so it doesn't actually become a part of the file, making it difficult for other applications to access the information. Moving forward, it may be necessary to actually trim the files in an audio-editing software to remove some part from the beginning so that it doesn't end up in the audiobook version.

Thanks for bringing this to our attention!