I’m pretty sure that to achieve this task, you must have employees assigned to both store’s cash registers and still be at least $100 profitable. However, the objective doesn’t specify that you must have employees at both locations.
Some people set up their second store and run it themselves, while their employees are running their first gift shop and then are confused when they don’t get credit for having two profitable shops.
This is supposed to be fixed in build 1369 (which should be up very shortly)! If it’s still broken after that, be sure to submit a new bug report, but hopefully it’s good!