Permission problems with command line CVS and Java CVS App

Greetings,
I'm part of a moderately sized website development team which recently upgraded to MacBook Pros (dual core) running OS 10.4.9. One of the primary tools we use in our day to day work is the open source concurrent versioning system (CVS). We've noticed a distressing issue running CVS on our macbook pros: there seems to be a problem with the way these new machines handle permissions on the directories/files that CVS uses to manage files.
The error occurs when the CVS application, in this case both command line CVS and GUI CVS application named SmartCVS, tries to rename a temporary file named Entries~ to its new name Entries (no ~). It looks like this:
java.io.IOException: Could not rename file
/Users/[USER]/Sites/[MODULE]/lib/CVS/Entries~ to
/Users/[USER]/Sites/[MODULE]/lib/CVS/Entries
at smartcvs.JP.a(SourceFile:125)
at smartcvs.JP.a(SourceFile:113)
We've noticed that if we open up a get info window on the directory we're downloading, and choose "Apply to enclosed items" right when we start the download process, the issue will be resolved, presumably because the permissions are being set on the subdirectories as the download is taking place.
We've checked the permissions on the overall ~/Sites/ directory numerous times, and they always seem to be set correctly as drwxr-xr-x. It's within this folder that CVS creates a directory with the CVS module name and downloads all the contained files, so we don't see why it would be having issues completing this successfully. We also checked to ensure the GUI CVS application is running under the current user on the machine: it does.
Has anyone run into issues like this in the past? Is there more information I could provide to further clarify the problem we're having?
Thanks for any input you have!

Thanks for asking Jeff, yes one place we are seeing this error is Java application SmartCVS, though the results posted here are from a normal command line CVS checkout.
===
Checkout command:
cvs co [MODULE]
===
Error:
cvs [checkout aborted]: cannot rename file CVS/Entries.Backup to CVS/Entries: No such file or directory
===
ID:
uid=502([USER]) gid=502([USER]) groups=502([USER]), 81(appserveradm), 79(appserverusr), 80(admin)
===
LS -ALN
Computer:~/Sites [USER]$ ls -aln
drwxr-xr-x 28 502 502 952 Jun 4 13:11 Sites
Computer:~/Sites/[MODULE] [USER]$ ls -aln
drwxr-xr-x 38 502 502 1292 Jun 4 13:33 www_root
Computer:~/Sites/[MODULE]/www_root [USER]$ ls -aln
drwxr-xr-x 32 502 502 1088 Jun 4 13:33 [SUBDIR1]
Computer:~/Sites/[MODULE]/www_root/[SUBDIR1] [USER]$ ls -aln
drwxr-xr-x 5 502 502 170 Jun 4 13:33 [SUBDIR2]
Computer:~/Sites/[MODULE]/www_root/[SUBDIR1]/[SUBDIR2] [USER]$ ls -aln
drwxr-xr-x 4 502 502 136 Jun 4 13:33 [SUBDIR3]
Computer:~/Sites/[MODULE]/www_root/[SUBDIR1]/[SUBDIR2]/[SUBDIR3] [USER]$ ls -aln
drwxr-xr-x 6 502 502 204 Jun 4 13:33 CVS
Computer:~/Sites/[MODULE]/www_root/[SUBDIR1]/[SUBDIR2]/[SUBDIR3]/CVS [USER]$ ls -aln
total 32
drwxr-xr-x 6 502 502 204 Jun 4 13:33 .
drwxr-xr-x 4 502 502 136 Jun 4 13:33 ..
-rw-r--r-- 1 502 502 45 Jun 4 13:33 Entries
-rw-r--r-- 1 502 502 45 Jun 4 13:33 Entries.Log
-rw-r--r-- 1 502 502 48 Jun 4 13:33 Repository
-rw-r--r-- 1 502 502 63 Jun 4 13:33 Root
MacBook Pro / MacPro Mac OS X (10.4.9)

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