Coming back to the emulator issue... I notice that by using the emulator the hard limit is 1 whereas with the dongle the hard limit is 65535.
Is that the reason why the software fails to use other functions that use additional licences/processes?
I am unsure if there is a workaround with the emulator.
EDIT: Eventually I found a way to extend the hard limit which completely solves the emulation problem!

I'll leave here an example in case it helps somebody else.
Using a Multikey registry dump, here's what it looks like:
So, the XXXX or the XX,XX are both the DevID for the dongle and the YY,YY is the dongle serial.Windows Registry Editor Version 5.00
[HKEY_LOCAL_MACHINE\SYSTEM\CurrentControlSet\Multikey\Dumps\XXXX0000]
"sntMemory"=hex:\
YY,YY,XX,XX,00,00,00,00,00,00,FF,FF,00,00,00,00,\
00,00,00,00,00,00,A9,3C,4F,06,DA,03,9F,AB,C4,3D,\
F1,C2,49,56,00,00,00,00,00,00,00,00,00,00,00,00,\
00,00,00,00,00,00,00,00,00,00,00,00,AC,31,00,00,\
45,24,13,00,05,00,05,00,05,00,03,00,01,00,00,00,\
00,00,00,00,00,00,00,00,00,00,00,00,00,00,00,00,\
00,00,00,00,00,00,42,34,00,00,00,00,00,00,00,00,\
00,00,00,00,00,00,00,00,00,00,00,00,00,00,00,00
"CellType"=hex:\
01,01,03,03,03,01,03,01,00,00,00,01,01,01,01,01,\
01,01,01,01,01,01,01,01,01,01,01,01,01,01,01,00,\
01,01,01,01,01,01,01,01,01,01,01,01,01,01,01,01,\
01,01,01,01,00,00,00,00,00,00,00,00,00,00,00,00
"Type"=dword:00000000
"DongleType"=dword:00000003
What changes the hard limit is the FF,FF you see in positions/bytes 11 and 12, the first couple FF alone set the limit to 255 and the second couple FF alone set the limit to 65280, if both are set to FF, then the limit becomes the sum of the two: 65535
The first group of bytes are interpreted as a normal number from 0 to 255 (00 to FF), the second group is interpreted as a multiplication by 255 of whatever value is set. Or something along those lines anyway...

Hope it helps, and thanks again to FoxB!