If the antenna or cabling is dodgy it can cause some of the RF transmitted by the AP to be reflected back into it and therefore causes interference. Using an amp means higher initial output and therefore stronger reflections, resulting in more degration of signal quality.
In your case as the amp serves a good purpose I then I'd suggest keeping it.

I just brought that up in my previous post as many people I have come accross who use them actually don't need to and create more problems for themselves in the process.
Back to the main issue, I agree with your points about obstruction or reflection being the probable cause. Note that materials such as concrete very quickly degrade performance if they are in the line of sight back to the AP. Reflections are a bit more difficult to detect and overcome.
A spectrum analyser is a good tool for helping track down sources of external interference and also how well you are receiving the access point itself. If you hire a wireless company make sure they have techs with some RF knowledge and gear, some companies simply send out a monkey with a laptop and NetStumbler.
If you think that the signal is being blocked by the actual building materials it may be worth investing in an extra access point to function as a repeater.