Saving a document problems

When navigating files to locate a target folder during a "save" folders are SOMETIMES grayed as though they are files. If I select one, it doesn't open. The file I'm saving acquires the name of the clicked folder, just as it would another file. As long as I navigate without using the Spotlight search box, I have no problems. I rebuild by Spotlight index and I reloaded the operating system on the AIR. Neither helped the problem. This happens on my 2012 MacBook Air and now, my new 27" iMac. I took my Air to the Genius bar where they performed permissions disk repair from an external drive, which didn't help. The Genius I saw said he never heard of this before. Both computers have fully upgraded Mountain Lion operating systems. It would seem that it is a software conflict somewhere, since I similar applications on both, but nothing exotic. I have a limited number of non-Apple applications on the new iMac.