Different definition of file version numbers in Jdev and Subversion

In the SVN Red book(http://svnbook.red-bean.com/), they say that updating a single file creates the new revision of the whole repository.
So even if a file has not changed, it still can go to a higher version.
+"Revision Numbers Are Different Now+
+In CVS, revision numbers are per file. This is because CVS stores its data in RCS files; each file has a corresponding RCS file in the repository, and the repository is roughly laid+
+out according to the structure of your project tree.+
+In Subversion, the repository looks like a single filesystem. Each commit results in an entirely new filesystem tree; in essence, the repository is an array of trees. Each of these trees is labeled with a single revision number. When someone talks about “revision 54”, he's talking about a particular tree (and indirectly, the way the filesystem looked after the 54th commit).+
+Technically, it's not valid to talk about “revision 5 of foo.c.” Instead, one would say “foo.c as it appears in revision 5.” Also, be careful when making assumptions about the evolution of a file. In CVS, revisions 5 and 6 of foo.c are always different. In Subversion, it's most likely that foo.c did not change between revisions 5 and 6."+
The above makes sense to me. But when I use JDeveloper with SVN, I see its showing me different version numbers with different files.
Can somebody explain. JDev essentially is showing the version of the file when it was last checked in, but because of changes in some other files, the "actual" version (as per the definition in redbook) might have changed...jdev DOES NOT show this change...why the apparent difference is what I want to understand.
Thanks,
Amit

Thanks for your replies.
@Timo - I checked out the project from SVN repository to a new folder. It still shows the old versions for some files. In other words, all files are not on same version as shown in app navigator.
@John - I have tried to reproduce the sections from the Redbook that I felt relevant and that led me to thinking what I am thinking (expecting) now.
--Amit

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using System.Collections.Generic;
using System.IO;
using System.Linq;
using System.Net;
using System.Net.Security;
using System.ServiceModel;
using System.ServiceModel.Channels;
using System.Text;
using System.Web;
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using System.Xml.Linq;
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[OperationContract(ProtectionLevel = ProtectionLevel.EncryptAndSign,
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get
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