I'm now a huge advocate of using package templates. For more info on how to use them see this post. Template provide a handy way to determine the best practices for your company and reuse those over and over again. Well there's one slight problem with using them. The package that uses the template inherits the PackageID of the template. Why is this a problem? Well, if you're using the System::PackageID variable for logging, all of your packages now will report that they are the template package.

So, you have two options. Ultimately, you must renumber each package to a unique value. You can do this manually in the package Properties pane. You can also do this in an automated method by using the dtutil.exe application and the /I switch as shown below:

The best way I feel is to create a batch file with the following code that will loop through every package in a directory and renumber it:

for %%f in (*.dtsx) do dtutil.exe /I /FILE "%%f"

Please note though that once you use DTSutil.exe to do this, it will re-arrange your package. Don't worry, your package will still work but the appearance may be a bit rearranged.

Note: You can vote to change the behavior of SSIS here to fix that problem: http://connect.microsoft.com/SQLServer/feedback/ViewFeedback.aspx?FeedbackID=241901