Yeah, GameGuru has issues with multiple folder levels, it's best to limit yourself to for example
mapbank/your title/your.fpe, the same with audiobank, scriptbank, and so on.
Also, when saving standalone, make sure you load each map into the editor and save it again one by one in reverse order, before hitting the save as standalone button, that helps to make sure all your levels are transferred.
i5, NV960 2GB, 16GB memory, 2x 2TB Hybrid, Win10.
i3 , Intel integrated graphics, 6GB memory, 512GB Generic SATAIII Win8.1.
Intel Celeron (duel Core), Radeon integrated graphics, 4GB memory, 180gB Generic SATAII, WinVista.
Q6600, Intel integrated graphics, 8GB memory, 512GB Generic SATAII, Win7.