Rebuild of Project not building all source files

Using 9i, I cleared all .class files from my target directory structure and then requested a Rebuild (right click project.jpr, click Rebuild project.jpr) of the entire project. I get a result that says there is one error (expected) and five warnings. When I look in the target library structure, I see that many of the .class files are not there.
I then do the same procedure for each package name (I'm showing the list of .java files using the Show Categories option), right clicking and rebuilding each package (over 50). This produces all the .class files.
Then, I can request a Rebuild of a given package on a subsequent date and JDeveloper will indicate that it compiled each of the source files in the package, but the create and modified dates of the .class files still show a previous date.
Can someone give a clue of what is going on? I expected Rebuild to build every class from every source for the entire project, when requested at that level. It certainly is NOT doing that for me.
Oracle IDE     9.0.3.10.76
UML Modelers Version     9.0.3.9.73
Business Components Version     9.0.3.10.62
SCM Support Version     9.0.3.9.73
java.version     1.3.1_02
java.home     C:\Program Files\Oracle\JDeveloper 9i\jdk\jre
java.vm.name     OJVM Client VM
java.vm.vendor     Oracle Corp.
java.vm.version     9.0.3.744 o
user.language     en
user.region     US
user.name     dvgreen
user.home     C:\Documents and Settings\dvgreen.NA
user.dir     C:\Program Files\Oracle\JDeveloper 9i\jdev\bin
ide.user.dir
os.name     Windows 2000
os.arch     x86
http.proxyHost     <no value assigned>
http.proxyPort     <no value assigned>
http.nonProxyHosts     <no value assigned>
ide.patches

I don't see anything on the Compile options that I would expect to affect this operation in this way.
No Ant involved. I'll just deal with it. I was hoping someone from Oracle might stop in here and be familiar with the issue.
As it is, I'm talking about recompiling a bunch of code that hasn't even changed. I just found it odd that it would report that it was compiling it, but not have any visible evidence to support the claim.

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