MCEBuddy is not able to find your comskip.exe
ERROR> 2014-04-17T13:32:22 MCEBuddy.AppWrapper.Comskip --> Application File Not Found : comskip\comskip.exe
Instead of replacing comskip, try something a better. Do a clean install of MCEBuddy. Extract your donor comskip to a directory (e.g. C:\\ComskipDonator)
The under Settings -> Expert Settings -> Custom Comskip, select the donator comskip in the directory you extracted it.