Check your project properties to see where are those files deployed.
Look at this picture:
http://apps.sourceforge.net/mediawiki/c ... Cofig8.png
(this is AFAIR from "Linker" at project properties)
It means theat if you have your Construct installed at:
Then location of project file must be one level below (for example C:\Program Files\Scirra\Construct\MyObjectCode).
Note that in SDK we've paths like:
..\..\IDE\Plugins\Runtime\Template.csx - for runtime
..\..\IDE\Plugins\Template.csx - for edittime (release)
Change those directiores to make destinations match.