Finder shows some but not all files in a folder

Question

In some circumstances, Finder only shows some (but not all) of the files in a folder. Why?
I notice this with Excel autosave files in the Office 2011 Autorecovery folder (Macintosh HD ▸ Users ▸ Conor ▸ Library ▸ Application Support ▸ Microsoft ▸ Office ▸ Office 2011 AutoRecovery). In my case, Finder shows 34 files but "ls" in a Terminal window reports 40 files. The missing files do not start with a period (.) and have the same permissions as other files that show in Finder (-rw-r--r--@ 1 <myname>  staff). Here's the last four lines of "ls -al" - the first two appear in Finder, but not the last two:
-rw-r--r--@  1 myname  staff    55296  8 Oct  2013 Word Work File D_1239425731.tmp
-rw-r--r--@  1 myname  staff    55296  8 Oct  2013 Word Work File D_1240072173.tmp
-rw-r--r--@  1 myname  staff    52796 13 Feb 11:08 safe1.xlk
-rw-r--r--@  1 myname  staff    95320 12 Mar 16:06 safe2.xlk
I have tried copying files from this folder to another folder, and/or changing their names. They still do not appear in Finder, nor are they visible in the File Open dialog of applications, even when the dialog is listing other files in that directory - but if I manually type the name into the File Open dialog, the app manages to find and open the file.
If I Spotlight-search for the file name, or search in Finder, without specifying that specific directory ("This Mac"), the file is not found, but if I direct the Finder search at that particular directory, then the search returns the relevant files.
So: why does Finder hide certain files when showing a folder, even though it can find and show those files if you specifically ask for them?
Now using OSX 10.10 (Yosemite), but I'm pretty sure I noticed this on OSX 10.8 as well.

Answer 1

So simple - thanks. I'd not been aware of the hidden flag, and now I've found the -O option on ls to display it.
Follow-on question: I now see that you can change the system-wide defaults to display hidden files with this...
     defaults write com.apple.finder AppleShowAllFiles -boolean true ; killall Finder
...but is there a way to specify this on a per folder basis? I'm happy enough to hide hidden files in general, but it would be nice if I could set an attribute/flag/whatever on the Office AutoRecovery directory that told Finder "in this folder, always display hidden files". Can I do this?