What is the difference between `open (-a) ` and double click in finder/spotlight? I recently installed leksah on my Mac (once directly, once via brew cask).

When I try to open it in Finder, Dock or use spotlight the window flashes open for a second and then closes immediately. 
When I open it via terminal using open -a Leksah or open ~/Applications/Leksah it opens just fine.

Other users have experienced the same issue with other apps and other OSX versions as well. Is there a difference in behavior when opening an application using any of these methods? How can one debug what's going on?
Well, one difference is that via Command Line, you can pass the file to be opened as an argument, but I guess this is not the difference you are after.

The behaviour you speak of appears to be a bug which can be observed when running Yosemite. The issue is still open: https://github.com/leksah/leksah/issues/37