Something with your project-files have gone amiss. I would suggest you to create a new project and copy&paste your programmed parts from the old to the new. The hardware setup must be done anew manually.
One of the easy way to do this is first print a project
datasheet which will give you all your settings for
each component in the project, then configing the
new project becomes a lot easier.
Also if making a new project does not fix problem,
consider reinstalling PSOC Designer. I would do an
uninstall first and manually delete all Designer pro-
gram directories after archiving your project in
another safe directory.
One other possibility before you go to all this effort,
do a clean and build of the project to see if that would
solve the issue.