Projection issues are often hard to spot and result in frustration for the programmer new to GIS developement as it is often necessary to go from one projection to another in order to have data lining up correctly. In my experience, there are a few projections you need to be aware of and this is going to help pass the first hurdle in more than 80% of the cases.
Those projections are:
-Geodetic (EPSG 4326)
-Google Map projection (Spherical Mercator)
-State Plane
-UTM
I suggest you check out the Code Community. There are a number of projects that show how to handle some concrete cases of having to work with those different projections.
I recommend:
code.thinkgeo.com/projects/s...basedonlat
code.thinkgeo.com/projects/s...stateplane
code.thinkgeo.com/projects/show/gpstogooglemap
code.thinkgeo.com/projects/show/geodetictoutmfly