The logistics add up fine if you assume that some poor decisions were made with regard to contracts which have no escape clause.
So your explanation is: BFL signed some bizarro contract with a shady supplier that is screwing them, but that somehow BFL can't lawyer their way out of it nor did they provide this explanation (which if true would completely absolve them of fault) to the community.
What probably complicated the process is the provision of chips to be mounted. This affects the board manufacturer's standard supply chain and I'd expect would attract higher costs for retooling and any custom processes involved.
Nothing on their boards is outlandish. Everything can be had from standard suppliers (like digikey). They at least got that part right.
This would in turn have affected the tendering process and may have resulted in selecting a manufacturer for the board who wouldn't charge as much for the custom aspects, but which can't do turnaround nearly as quickly.
There is nothing custom or crazy on the board, it is actually quite simple and straightforward.
Notice that the people doing BFL DIY boards completed their projects and got them hashing in a short time with few problems.
Can't comment on the first as it is mere speculation. It does fit pretty well, as we've all seen the issues with stock of power supplies, chips not being delivered on time, etc.
Lawyers are expensive, and very few companies will come out and say they got screwed by a supplier due to the effect it has on peoples perceptions of them. Personally if it was the case that BFL did get screwed by their suppliers, I'd be happier if they did come out and say it, as it would then silence a lot of the whining on forums such as these. Chances are though, if they did come out and say it at this stage they wouldn't be believed anyway, so that might be another reason why they say nothing.
The basic board components aren't unusual, sure. The custom ASIC however is, and that might have instantly turned off some manufacturers, who would either turn down the opportunity or simply price their tenders higher to avoid being awarded the contract (this happens in all avenues of business, not just electronics and IT). They see it as a risk they would rather not take.
The DIY boards have one massive advantage - they have the lessons learnt from BFL and its boards shemozzle. They know the true power consumption of the chips upfront and can design the power supply to suit. They have reference designs from BFL to work with too, if they want to be extra lazy. Lastly, they aren't working with the kinds of quantity that BFL is. The hardest work has already been done for them.