I am using a refractometer to determine gravities. I am aware of course that values measured need to be corrected depending on OG of the fermenting batch. What I don't know is, what kind of sugars am I measuring. Am I only measuring fermentable sugars or also non-fermentables, i.e. should the measured final gravity of a malty beer be higher than the one of a really dry beer? Or is the measured final gravity only dependent on the yeast/attenuation?
A refractometer works on the principle that a sugar solution has a different index of refraction than water, thus the concentration of a sugar solution can be determined with the instrument.
Due to the relatively similar indices of various sugars, it will measure all sugars, as well as other non-fermentables.
Because ethanol has a very different refractive index than sugar, a refractometer cannot directly be used to measure a post-fermentation beer. As you mentioned, the value read by the refractometer must be adjusted, as in this post.
And yes, a maltier beer will read higher than a dry beer, both before and after compensation, assuming they have the same concentration of alcohol.
The refractometer measures the sugar concentration of a particular liquid. It will register both complex and simple sugars. Once fermentation begins the presence of alcohol distorts the refraction thus requiring you to use a conversion chart or calculator to determine the remaining sugar. To do this you will need to know the original gravity. The measured final gravity is just the remaining unfermented sugars still in solution.
Here is the calculator that I use http://brew.stderr.net/refractometer.html.