I only know the big companies and they're quoting a lot higher than I usually pay here for similar roof. 

The seller agreed as long as we agreed to the asking price, there was a patch needed in the roof and a door had to be replaced.

I made minor repairs to mechanicals and replaced an aging garage roof but didn't really invest much else.

could it be the roof valley?

I would be getting an inspection so any roof or foundation issue would blow it out of the question.

I went in using the % rule, since I had a good understanding of rehab costs and enough cash to carry me through even if the rehab cost double.If you truly reserve for everything, i.e. a roof has a 25 year life and will cost about $7,500, that's $25/mo each month if you have a new roof. 

In practice, I have seen roofs that were well beyond their service life and needed immediate replacement pass a conventional appraisal without being mentioned by the appraiser.

Seller financed deal at $40,000 bathroom was down to studs, kitchen had no flooring and cabinets were falling off at the hinges, no gutters on rear of home, rear entry door suffered a break in and roof was leaking prior.

Water intrusion into any part of any physical structure on the Property; leaks from or in any appliance, pipe, slab or roof; standing water, drainage, flooding, underground water, moisture, water-related soil settling or slippage, on or affecting the Property?

I'm looking at using Formula Roofing to replace my roof and install a skylight in my rental property.