Spotlight/Finder can't find a file, yet when I search the timecapsule for they find it. If I try to restore the file I get "file with that name already exists...." What is wrong?

I was trying to find a file (iTunes Backup). When using finder/Spotlight they couldn't find the file.
I then opened up my timecapsule and searched for the file....tick-a-de-da it found it in yesterdays backup. I attempted to restore the file and got the prompt "A file with that name already exists in this location, would you like to keep both, replace the file or cancel the request.
So if the file is there why can't spotlight/finder find the file??
If it helps I get this from the terminal when checking if indexing was enabled.
$ mdutil -s -a
Indexing enabled.
/Volumes/Data:
2014-11-18 18:09:39.542 mdutil[1472:572531] Metadata.framework [Error]: mdsCopyStoreAttributes failed: (8) (os/kern) no access
No index.
/Volumes/Time Machine Backups:
Indexing and searching disabled.
/Volumes/Time Machine Backups/Backups.backupdb:
Indexing enabled.

Hi Danielle,
Is there any possibilty that some of your files (a VI or DLL?) have been moved, renamed, or deleted? Also, what version of LabVIEW are you using and are you using any .NET DLLs? Another option to consider would involve VISA or DAQmx property nodes. Are you using any of these property nodes in your code? Here is a KnowledgeBase article to describe more about the VISA and DAQmx property nodes in a source distribution:
Error Creating Source Distributions Involving rc Files: http://digital.ni.com/public.nsf/allkb/833BFD5E9CA0224886257584004DAA4C?OpenDocument
I hope this is able to help.
Anna L
Applications Engineer
National Instruments

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