I also have this issue and have managed to fix it using the instructions in this thread
I was unable to download the attached zip file with the updated .exe file as I was not permitted to view the attachment so I followed the steps below
1. Download and install Wherigo Builder
http://www.Wherigo.com/builder/download.aspx
2. Download and install .NET Framework 2.0 Software Development Kit (SDK) (x64)
http://www.microsoft.com/downloads/details.aspx?familyid=1AEF6FCE-6E06-4B66-AFE4-9AAD3C835D3D&displaylang=en
3. Run command prompt with administrator privileges and ran the following command
"C:\Program Files\Microsoft.NET\SDK\v2.0 64bit\Bin\CorFlags.exe" /32BIT+ "C:\Program Files (x86)\Groundspeak\Wherigo\Builder\WherigoBuilder.exe"
My previously saved .lua files now seem to open without error although at the moment they only contain a name an initial coordinates