Is there any other way to structure the deal to avoid these elements?

This site was extremely useful for me and I used it numerous times.  

Essentially when you are purchasing a property to flip; you are (presumably) purchasing that property at a discount, so that after your repairs (known as ARV - After Repair Value); the property will appraise for more than your: cost to purchase the property + cost to rehab the property.In numerical terms, say in an area, the median home is selling for $550k and you can get a property for $280k + $125k in rehab and holding costs (insurance, escrow funds, agent commissions, etc), that will = $405k that you've paid out of pocket.

Here in NJ, there have been (from what I understand from talking to other realtors) numerous times where short sales have come onto the market, and the buyer and seller agree, then the bank kills the deal and forces it into their auction site so that they can give themselves a 5% premium on the back end since they own that site.  

This is an alternative to a developer having to take out numerous individual properties within a large property purchase that they intend to sell in individual parts.

I have no experience, but have spent a considerable amount of time watching numerous televised shows about home flipping, and ive read some on the subject. 

I doubt you would have ignored the red flags if you had numerous deals on your plate at the time to choose from.

After numerous voice mails and emails I finally get an email response from one of them and all they say is that they are looking into it.

There are numerous hardships such as your career forcing you to move out of the area that they have programs for.

There are numerous banks or credit unions that will do a secured card with pretty horrible credit.