Issue and Workaround for Syncing to iPhone
I went to Apple's lab in Cupertino on July 20 and confirmed that if you add or move Safari bookmarks in Bookdog 4.2.12 or earlier, do not add any properties in the Inspector, save your bookmarks and then immediately sync an iPhone before editing bookmarks in Safari, the iPhone will not pick up the new or moved bookmarks.
This issue should now be fixed, in Bookdog 4.2.13 or later. Please let me know if you have any more trouble with iPhone syncing.
Bookdog Recommends: Use Safari 3.0 on your Mac
Although I can't find any warnings from Apple, if you are syncing your Safari bookmarks with the iPhone, you should update the Safari on your Mac to the Safari 3.0 beta. The reason you want to update is that Safari on your iPhone is 3.0. Safari 2.0 does not support bookmarks at the root (Collections) level, but Safari 3.0 does. Since adding bookmarks at root level is the default behavior on the iPhone, upgrading to Safari 3.0 will ensure that you'll always see new iPhone bookmarks in the same place as on your Mac and vice versa.
Even after updating to Safari 3.0, note that the four "default" bookmarks that come in your iPhone will always appear at the bottom of the your Bookmarks root level in your iPhone: Apple, Yahoo!, Google and My AT&T Account. These bookmarks will not show in Safari on your Mac and will not show in Bookdog.