I've just had a thought. The config setting you've set will prevent NCrunch from triggering builds when .ts or .html files are changed, but they won't prevent NCrunch from triggering builds when the IDE touches other files on the file system as a result of these files being changed.
For example, something quite new that I noticed in the IDE is that when you save a file to disk, it won't actually save over the original file being saved. Instead, it saves the file under a temporary name, removes the old file, then renames the temporary file over the old one. This caused several problems with NCrunch's change detection, as CPS uses recursive wildcards to include files in the project, and NCrunch wasn't able to tell the difference between VS saving an already included file as opposed to VS creating other files that should be included in the project. This specific use case is now handled by NCrunch (the temporary files are ignored), but it illustrates the sort of problems that the new CPS file inclusions have introduced when we have a development environment that regularly creates temporary files under the project path.
If you turn on the 'Log to output window' setting and set the log verbosity to 'Detailed', NCrunch will report in the logs which files it's detected as changed prior to kicking off a build or project reload. If you find this problem happening again, I'd recommend reviewing the logs to see if you can find any patterns in files on disk being changed by the IDE.
