I am using emClient on two different installations (Games, Work) on the same physical machine (no virtualization). The emClient database is stored on a data partition which is accessible on both Windows Installations when active.
Everytime I am switchting the Windows Installation I have to reenter the serial.
That means your license check is hyper sensitive. Checking the CPU serial should be sufficient to judge that the lincese is running on one physical computer.
That is the reason why I never moved to the Pro version.
The license information is not stored in the user database. And because separate OS installations on the same hardware generate different hardware Guids, the license manager sees this as two separate computers. Which they technically are.
You can use a single license on a computer with multiple user profiles though.
If you have a Pro License, open a support ticket, and maybe the developers can find a solution for you. Otherwise, the Free License option Jay suggested is the way to go.