Here's a zip file that replicates the issue.
There is a "sourcenew" which contains a newer version in which there are only two changes. There is a change in the "History" and in the value and default value of the "Default Temperature Cluster" in "sub.vi".
You should be able to bring up "sourceorig\TestComp.lvproj" or "sourcenew\TestComp.lvproj". Once one of them is opened, you should be able to open the "source" folder, then the "TestComparison.llb" and then open "main.vi". If you want to run "main", click the run button and click "Go". It will open up "sub" and will allow you to click "Change Begin", "Change End", or "Done". If you click "Change Begin", it will bring up "subsub.vi". You can change the units or the beginning value. When you click "Done" the beginning value will become the default for the ending value. In "sub", you'lll now see the three values. When you click "Done" in "sub", you'll return to main and can wait 8 seconds for it to end.
If you run "sourceorig", the default values that shows in "subsub" will be "F", "70", and "70". If you change those values and close down (and then close main and bring it back up), running again will go to the same defaults. On the other hand, if you run "sourcenew", those values will come up as "C", "20", and "20" and will likewise stay as defaults.
If you compare the two hierarchies, the comparison tools will show that there was a "History" change in "sub" between the two versions, but it will not show the default value change.
Hope that helps!