Your mistake was, you upgraded from XPro 5 instead of just regular X5. If you have X5, your $99 buys you the manual and the upgrade to version 6. However if you have XPro 5, your $99 buys you the upgrade but no manual (but feel free to give them an extra $30 if you want one). The savings on upgrade is 33% more cost effective for you if you haven't previously paid for the pro upgrade. This is explained on the upgrade page; you only get the manual if they've never sent you one before or you pay them extra to include it.

Of all of the copies of Xara I've purchased over the years (going back to 2.0) only one ever came in a box, and that was shipped in an Envelope so it was smashed flat by the time it got here. I don't remember getting anything other than disks in a plastic/paper sleeve and the new keyboard shortcut chart apart from that (one version came in a regular jewel case, but I can't remember which; I think it was whatever version came in the box).