Here’s how I finally got the source code to build for the WIZ550S2E firmware. This was run on a WIN7/64 bit computer.
Downloaded the source code for this module from github.com/Wiznet/WIZ550S2E. I downloaded the zip of the entire repository, then extracted to a folder on my desktop.
Used “Import Project” under the “Quickstart Panel”. Clicked browse next to the box “Project Directory (unpacked)” and selected the downloaded code on my desktop. It found all four projects. Clicked options for “Search for nested projects”, and “Copy projects into workspace”.
Right Click on each project -> Properties -> C/C++ Build -> Builder Settings -> “Generate Makefiles automatically” 
Right Click on each project -> Build Configurations -> Set Active -> Release 
Right Click on each project -> Clean Project
Build project 
Right Click “lpc_chip_11exx” project -> Build Project
Right Click “wiznet_s2e_wiz550s2e_board” project -> Build Project
Right Click “WIZ550S2E_Boot” project -> Build Project
Right Click “WIZ550S2E_App” project -> Build Project
Boot HEX is located here: [LPCXpresso workspace]WIZ550S2E_Boot\Release\WIZ550S2E_Boot.hex
App HEX is located here: [LPCXpresso workspace]\WIZ550S2E_App\Release\WIZ550S2E_App.hex
 = Can’t build WIZ550S2E_Boot
 = This step might not be necessary, but the compiler ran out of program space (firmware too big) until I tried this.
 = See “The order of compile” on github.com/Wiznet/WIZ550S2E