Steps to reproduce:
1. create new C/C++ Project with Existing Sources
1.1 select Custom Configuration Mode
1.2 specify path to files with wrong register
1.3 follow wizard
2. Call Find in Projects and specify some string that exists in .h files

The result:
No .h files found
Expected:
All files with specified string are found

If in step 1.2 specify project path with correct register, it works OK

I'll attach two projects created as described above and sample source code. 
Note that if shut down NB, replace the bad project with good one (or just and start ND, issue remains. 
Thus, there is some data outside project directory that causes wrong behaviour.