Menu item showing accessible in Simulate Navigator for certain role doesn't actually show up in Navi

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As the title described, anybody came across such issue and how did you solve it?

Problem Description
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Data Exchange used to be hidden by setting up from Tools > Structure. We later modified the setup to make it visible (both Visible and Springboard are set to Yes)
To simulate navigator for one our custom HR role, we see Data Exchange is accessible, however, login by a user with this role, Data Exchange doesn't show up.