I'm running into the same bug others have reported here on the forum. I've noticed Exp++ is not showing hidden files and folders, despite the fact the Exp++ settings are set to show all files. Through some testing I've found if I disable hidden files in Windows Explorer then all of a sudden Exp++ starts showing hidden files/folders. So for me, the setting in Exp++ to show hidden files does nothing, it seems to rely on the Windows Explorer setting. Others posts said this can happen if you're running Exp++ as another user, or right-click run as Administrator. I am not running Exp++ as another user, nor am I using the right-click run as admin - although I do disable UAC on my systems which might be the same thing as always running as admin. Either way, that shouldn't matter. Exp++ shouldn't depending on Windows Explorer settings, that's counter intuitive to the whole idea of running a Windows Explorer replacement program like this.
I've reproduced this problem on the following systems:
Windows 7 SP1 x86 using Exp++ 1.3.5 32-bit
Windows 7 SP1 x64 using Exp++ 1.3.5 64-bit
Windows 8 x64 using Exp++ 1.3.5 64-bit
Windows 8.1 x64 using Exp++ 1.3.5 64-bit
Let me finish with a little praise. I LOVE Exp++, such an awesome program! Hands down the best Explorer replacement program out there, and I think I've tried them all. Keep up the great work.