If they won't manage a property because of the neighborhood, then I know that is a red flag for me to avoid.4.

The previous owners did a do-it-yourself remodel which had tons of red flags if I had taken the time to cross-reference the sellers disclosure with the inspection report, but at that time the market was hot and I had to move fast.

To me this is very market dependent and product dependent.. in our Market some developments that are red hot that Lennar owns they might only offer 5k on a 600k sale.

Red flags yet?

And when a property cycles back to the market, it's not always a red flag – sometimes it's just market dynamics at work.

However, when you look at the Affordable Housing website, only 4 out of 32 available properties that accepts voucher are listed by $1,550 or more.Is that maybe a red flag that there's no demand for Section 8 in Cleveland? 

But there are also some real challenges, like dealing with lower tenant quality on average, the extra red tape, annual inspections, and the longer time it takes to get tenants placed compared to the open market.

Though fee schedules vary by company, generally speaking, you'll pay more up front for checkbook control and less over time, since the full custodial companies will have transaction fees not to mention the red tape of going through the custodian for all transactions. 

Or would this raise red flags for conflict of interest? 

You can't purchase the software stand-alone (red flag for someone with some experience).