The 3 executables listed in the ftp site are meant for specific functionalities. In order to install SPIController software please click on SPIController_Setup.exe.
The functionalities of all the installers are explained below.

1. SPIController_Setup.exe : This is the executable that installs SPIController software on your machine. 
This is the only installer that should be run by the user. The other 2 are  not meant for manual installation. 

2. SPIController_Setup_Base.exe: This executable should not be manually installed on the machine.
This executable is meant for updating the SPIController software with new/modified SPIController configuration files or the latest dlls.
This executable is called by the SPIController upon clicking File -> Download Files From FTP site if the current software in the machine is out of date.

3. HadBoardSetup.exe: This executable should not be manually installed on the machine.
This executable contains the dlls associated with Hadv6. These dlls will be automatically installed along with the SPIController with the version 
higher than 1.0.90.3. Prior versions can get these updates upon clicking File -> Download files from FTP site. 