Can't search inside some folders

[irsdl]

Hello
I downloaded a folder that had some php files to my computer by using a perl script. This application cannot search inside those files. I have checked file permission to make sure my user and admin have full control; also I ran NCC code navi with admin permission but I got no result (it can show the PHP codes if I browse to those file in NCC code navi app).
However, if I download a zip file by my browser and extract it, it works fine and it can search inside the files.
Unfortunately I cannot give you more details about the files and I don't know if you can replicate this issue or not. I guess it is related to files attribute but I am not sure.
I am using Windows 7 64b with NTFS.

Thanks

[irsdl]

I resolved this problem by doing this: I copied all the files/folders that were inside the root folder to another new folder! (renaming original folder didn't work, compressing the original folder and extracting files somewhere else didn't work).

[irsdl]

I renamed the new folder to the original name, now it does not work again even if I rename it again! I am thinking that I am doing an easy mistake here...