When you create a copy of your data file using:
File → Copy or Backup File … → Create a copy or template
The new data file is supposed to be completely separate from the old data file you copied from.
But it keeps using the same folder name in C:\ProgramData\Quicken\Inet.
For instance, if my original data file name is "Current" there is a folder:
C:\ProgramData\Quicken\Inet\Current
If I make a copy of that data file and call it say "TestCopy" that copy keeps using C:\ProgramData\Quicken\Inet\Current. This means that the two data files will be sharing all the files in that folder including runtime.dat which can really mess up what the user sees for certain statuses in Quicken.