Yeah they screwed up a run probably trying a cheaper vendor. But at that point had already produced a greater quantity of quality runs than Another World. And now are back on track it seems and still producing more.
And taking into account every Skunkboard is probably twice as involved to produce as a game cartridge it chews up even more the limited run because of x,y and z excuses.
I am not sure how you think a Skunk is more involved? Putting components onto a board isn't rocket science, and majority of Skunk components are surface mounted, possibly even put on at the same place as the boards are printed, if not whilst small SMD soldering isn't rocket science. Putting the code onto the skunk (BIOS and Firmware) will most likely be done via JTAG simply enough, once the board is assembled (assuming this isn't also done at the factory). And that's it, ship it...
I *think* the AW carts are not your regular carts, so construction pretty similar, done at factory. SMD. But programmed via a Jaguar or custom programmer. Once programmed each one needs to be tested. At this point if they were shipped, yeah same as a skunk roughly... BUT.. they all now have to be put in shells, have a sticker put on (carefully), and added to a box, there is the cart carrier in the box, and the manual, and the box itself.
So that's Label, Box, Manual, Inner, and cart shell.. all extra on top of what is required for a Skunk... All those printed materials are likely to not be available in orders of 10 or 20, or even 50 at a good quality. You will also need to get the boxes cut out, so you may need a template made for the printers to use to cut the boxes. The boxes will all need to be folded and glued, manuals will need to be cut, folded and stapled/glued. Before you get anything printed you need to find a willing and suitably equipped printer, get a valid deal (for your 200+ boxes minimum order), get proofs made to ensure you are not going to buy 200 boxes where the colours are off, same for the manuals, and labels.
Once you have gotten all of that, you need to put those boxes, inners, carts, labels and manuals into one another, use the stock of postage materials you have also had to buy, and then one by one send out each of those boxes you just spent hours building up.. and then take all of that to the post office?
Yeah, totally the same as getting a board made and posting it out bare / in a plane box that.
Plus there is the added stress of having to deal with unhappy customers, any possible fails that happen after they have been sent, lost in the post items (insurance, cool, because the insurance company will go and rebuild those missing carts for you? oh wait no, they'll argue and maybe at some point give you some money back, you still have to redo that effort to send out another copy, hope you have enough parts left!)
And a skunk appeals to more people (I'd imagine). I have more fun with my Skunk than any single Jag title, It is useful to many people for many reasons, a game is only that one game, so more limited appeal.
Misjudge any of the above and you could end up losing a load of money on wasted materials and time.
Producing a high quality release is NOT a simple, easy thing. Especially if it's something you have created.