The point is that you need to run the app through the JRE, not the JDK. It probably doesn't matter which install the JRE came from, then again they may not be identical, so it might be worth a try?
Datpacking is a straightforward enough process, if it's not outputting a packed file, I can only assume there is an issue somewhere with compatibility and your system. Because a JAVA app isn't installed code, it's just run from it's container, that really shouldn't be a problem. Of course if changes in Java have led to an issue with the code, you may find an older version of Java works? But frankly I'm just speculating here.
I guess the first thing to check is whether it can dat pack any files at all, or if the issue is specific to SimCity_1.dat. Given that's a really large file, it takes more resources to handle the operation. After that make sure you have full permissions for running the app and accessing the input/output folders. From the command line you may need to use SUDO to elevate the permissions given to the app. Otherwise be sure you are checking the correct output location for the dat packed files.