Hello,
I'm also seeing the cloned kerbal issue when doing EVA and then re-boarding. It seems mostly harmless... except they can become orphaned, potentially blocking the command module hatch or preventing certain actions by the original kerbal.
I ran a test on a fresh installation, with no mods other than KKS and ModuleManager. Platform is Windows 7 x64, no 64bit file replacements or command line options, etc. There are exceptions in the log, as in Matt77's post. Mostly a giant pile of these...
FileNotFoundException: Could not load file or assembly 'KIS, Version=1.2.3.0, Culture=neutral, PublicKeyToken=null' or one of its dependencies.
I can link to the full copy of the log if needed.
Enjoying the mod, looks really promising. Thanks