Jinitiator becomes corrupted, application closes

We have applied ATG RUP 6 to our 11.5.9 instance, upgraded to JDK, upgraded JInitiator to, and migrated the web/app tier to Linux. This has been deployed to about
40 users, and of that, 4 have had issues with JInitiator. They are able to log
on to the app, but when they select a responsibility, any responsibility, all of
the windows close. This is consistent behavior, and is only corrected when
JInitiator is reinstalled.  Digging further, we found that 3 files on the client workstation are modified when this occurs.  The files are in D:\Program Files\Oracle\JInitiator\lib.  The 3 files are i18n.jar, jaws.jar, and rt.jar.  Before the problem occurs, they look like this:

02/05/2008 02:28p 5,755,020 i18n.jar
02/05/2008 02:28p 1,021,387 jaws.jar
02/05/2008 02:28p 12,337,452 rt.jar

After the problem occurs, they look like this:

8/7/2007 1:37 AM 0 i18n.jar
2/4/2008 2:16 PM 5,755,020 i18n.tmp
8/7/2007 1:37 AM 0 jaws.jar
2/4/2008 2:16 PM 1,021,387 jaws.tmp
8/7/2007 1:37 AM 0 rt.jar
2/4/2008 2:16 PM 12,337,452 rt.tmp

Apparently the original files are renamed to have a .tmp extension, then new 0 byte files are created in their place.  We don't know what is causing this...  Has anyone else seen this?  Any suggestions for isolating the cause?  
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What happens when you copy over those 3 files from a machine that is working properly?  Also, what happens when you manually rename them to their original config?

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dbafhAuthor Commented:
If we put the 3 original files back, the application starts working again.  Likewise, if we rename the .tmp files to .jar files, the application starts working again.
well, attached below is a batch file for them to click on instead of the application's shortcut. You'll need to replace items within the <> delimiters with the parameters where:
"executable path and executable" will look something like this:
  start "C:\program files\myob11\myob.exe"

This link can be found from the start-bar shortcut (right-click-->properties-->and copy the target)

The code will take all the newly created junky .jar files, and will rename them to a .jar.bak
Then it will take all the .tmp files and rename them to .jar
Then it will execute the applicaiton.
When your applicaiton closes, it will rename the good .jars to .tmp and will create new .jars
When you execute the code again, it will over-write the old .jar.bak files with the new trash files and will restore your jar files from the tmps.

It's a work around, but it may be more convenient than doing this manually.  This script will remain "under the covers", so to speak.
@echo off
set myobjar=D:\Program Files\Oracle\JInitiator\lib
for /f "usebackq" %%i in (`dir/b "%myobjar%\*.jar"`) do move /y "%myobjar%\%%i" "%myobjar%\%%i.bak"
for /f "usebackq delims=. tokens=1*" %%i in (`dir/b "%myobjar%\*.tmp"`) do ren "%myobjar%\%%i.%%j" %%i.jar
start "<executable path and executable>"

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dbafhAuthor Commented:
I appreciate the suggested solution, but it didn't really help determine the source of the problem.  We did finally determine the root cause - an errant SMS package was attempting to reinstall the jinitiator on affected workstations repeatedly.  Once we got that shut off, the problem went away.
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Windows XP

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