Sorry for the lack of response. It isn't possible to monitor questions in the arduino forum due to the volume of discussions.
It would be good to work through this issue in the visual micro forum which is dedicated for the visual studio plugin.
Having said that the plugin is designed for microsoft windows users and dev time is limited. Currently dev is working towards arduino 1.5 + chipKit, wiring etc.
We can't slow down dev for Apple Mac users but if you would like to help us get to the bottom of this issue then we will try to find the time.
The only setting that the Visual Studio plugin uses from the arduino ide is the "Sketch Book Folder" path. The simplest fix might be to let you set this path in the Visual Studio options thus removing the need for the plugin to look at the Arduino config.
Does this make sense? If so and if you would like to see this work completed then please raise a thread in http://www.visualmicro.com/forums