However (and this is important!) I am now at a position when just opening a file from the build machine in Visual Studio may necessitate a reboot to make VA work as intended.
Upon opening a file, parse all other unparsed files in the same directory: VA Options -> Projects -> File Handling -> if Solution is empty VA Options -> Projects -> File Handling -> if Solution is not empty
VA_X.dll file version 10.6.1810.0 built 2010.01.22 DevEnv.exe version 8.0.50727.762
VA Options -> Projects -> File Handling -> if Solution is empty -- was ON (now OFF) VA Options -> Projects -> File Handling -> if Solution is not empty -- was OFF
Lets start by looking at the Find Symbol dialog box. This has a checkbox "Show only symbols defined in current solution", is this turned on of off? Turning this on should fix the problems you are seeing with this dialog.
When you open a code file that is not part of the solution VA parses it. So it learns about the symbols in this file. However it will forget about these symbols when you rebuild VA symbol database.
So the fact that you were seeing this problem after doing a symbol database rebuild bothers me. Is it possible the IDE was remembering that you had opened files from outside the solution, and it was opening these files when you reloaded the solution? Thus showing VA these unwanted symbols again?
For Find References, if you turn on:
VA Options -> Advanced -> Refactoring -> Display project nodes in Find References results
does this help? Are the unwanted symbols separated out from the wanted symbols?