I've seen the same thing on some of my own Shapeways orders.
In particular, I noticed that any delay for Niagara/Lawrence 1/1000 scale kits seemed to involve the foremast. It's the smallest part in the kit, less than half the size of a toothpick.
Shapeways uses printers that have bins of plastic powder in them. When the laser or whatever it is hits the powder, the parts gradually emerge from the dust. Their engineers consolidate dozens of parts from many different customer orders in a single batch, to make the printing as efficient for them as possible. I've seen videos of it, and each binload looks like a giant interlocking puzzle that they fit together.
When they take the parts out of the bin, they have to remove any support material and clean the parts off, then pack each one for shipping. So I they tell me it's very easy for them to lose a super-small part, or to mistakenly trash it along with waste material. That's how they lost the mast in my own first order. I later had them reprint it and I'm waiting for it now, along with two Royal George kits.
I think their fulfillment process isn't "first come, first served," but follows some other internal logic -- maybe it just depends on how they decide to put together a certain printing batch at a given time.
They need to get better at handling tiny parts. Particularly since so many of the designers who use Shapeways make jewelry and other small things.
I probably increased the chance of glitches by selling multi-piece kits instead of 1 ship=1 part. But then the designs could never look as good as they do. A single-piece ship would have to be very chunky and distorted in order to print, and would look more like a little game token than a scale model.
But I hope you see your model soon and enjoy it. Thanks for trying it!