KSP Mods not loading after manual install win7

Manually installing KSP mods by unziping them into a KSP GameData folder is not working for me. Does anyone understand why this would be? As I understand it, you unzip the mod and drop its mod directory into GameData to look like this. And then restart KSP.

ls -l "/ms/c/Program Files (x86)/Steam/steamapps/common/Kerbal Space Program/GameData"
total 8
drwxrwx---+ 1 pete None 0 Jan 29 16:15 KerbalEngineer
drwxrwx---+ 1 pete None 0 Jan 24 21:44 MechJeb2
drwxrwx---+ 1 pete None 0 Dec 17 15:24 Squad
drwxrwx---+ 1 pete None 0 Jan 26 19:33 SquadExpansion

I installed both KerbalEngineer and MechJeb2 and neither worked. I used ckan.exe to reinstall KerbalEngineer and it worked, but I would rather install these plugins manually. KSP is a Steam managed ver 1.11.1.3066.

If I inspect GameData with cigwin terminal the KerbalEngineer dir that ckan.exe installed looks exactly the same as what I had previously put there manually. Take a look at the md5sum checksums of the files from the unzip and the files that CKAN put in GameData. They are the same files. Does anyone get what is failing or know how to debug this ?

Contents of the zip (unzipped)

$ md5sum /ms/c/Users/pete/AppData/Local/Temp/KerbalEngineer-1.1.8.3/KerbalEngineer/*
md5sum: /ms/c/Users/pete/AppData/Local/Temp/KerbalEngineer-1.1.8.3/KerbalEngineer/AssetBundles: Is a directory
5ffba2a1c5be09e579eb9bb4fe700aac */ms/c/Users/pete/AppData/Local/Temp/KerbalEngineer-1.1.8.3/KerbalEngineer/KerbalEngineer.dll
1e5a38f246306acfba5066a9ba990290 */ms/c/Users/pete/AppData/Local/Temp/KerbalEngineer-1.1.8.3/KerbalEngineer/KerbalEngineer.Unity.dll
0847444c8ef98576f0311179fd6b3a2d */ms/c/Users/pete/AppData/Local/Temp/KerbalEngineer-1.1.8.3/KerbalEngineer/KerbalEngineer.version

md5sum: /ms/c/Users/pete/AppData/Local/Temp/KerbalEngineer-1.1.8.3/KerbalEngineer/Parts: Is a directory
md5sum: /ms/c/Users/pete/AppData/Local/Temp/KerbalEngineer-1.1.8.3/KerbalEngineer/Presets: Is a directory
md5sum: /ms/c/Users/pete/AppData/Local/Temp/KerbalEngineer-1.1.8.3/KerbalEngineer/Settings: Is a directory
md5sum: /ms/c/Users/pete/AppData/Local/Temp/KerbalEngineer-1.1.8.3/KerbalEngineer/Textures: Is a directory

Files installed by CKAN. The hashes match

$ md5sum /ms/c/Program Files (x86)/Steam/steamapps/common/Kerbal Space Program/GameData/KerbalEngineer/*
md5sum: '/ms/c/Program Files (x86)/Steam/steamapps/common/Kerbal Space Program/GameData/KerbalEngineer/AssetBundles': Is a directory
5ffba2a1c5be09e579eb9bb4fe700aac */ms/c/Program Files (x86)/Steam/steamapps/common/Kerbal Space Program/GameData/KerbalEngineer/KerbalEngineer.dll
b68d7b2bb6663c06dc1f8a9ed892f476 */ms/c/Program Files (x86)/Steam/steamapps/common/Kerbal Space Program/GameData/KerbalEngineer/KerbalEngineer.log
1e5a38f246306acfba5066a9ba990290 */ms/c/Program Files (x86)/Steam/steamapps/common/Kerbal Space Program/GameData/KerbalEngineer/KerbalEngineer.Unity.dll
0847444c8ef98576f0311179fd6b3a2d */ms/c/Program Files (x86)/Steam/steamapps/common/Kerbal Space Program/GameData/KerbalEngineer/KerbalEngineer.version

md5sum: '/ms/c/Program Files (x86)/Steam/steamapps/common/Kerbal Space Program/GameData/KerbalEngineer/Parts': Is a directory
md5sum: '/ms/c/Program Files (x86)/Steam/steamapps/common/Kerbal Space Program/GameData/KerbalEngineer/Presets': Is a directory
md5sum: '/ms/c/Program Files (x86)/Steam/steamapps/common/Kerbal Space Program/GameData/KerbalEngineer/Settings': Is a directory
md5sum: '/ms/c/Program Files (x86)/Steam/steamapps/common/Kerbal Space Program/GameData/KerbalEngineer/Textures': Is a directory

Do they need to be registered in the registery?