I've tried to include as much information as possible, but if it isn't relevant I will remove it.
I purchased a Raspberry Pi 4 months ago, and I've been using it to run some CRON jobs. I have a Logitech keyboard and mouse, which I used with the Pi during the initial week, but haven't connected them since, because running it headless was easier. Last week, I decided to start using the Pi as a media server at home and connected it to a Hard Disk (NTFS). Now because my TVs won't recognise some video file formats over DLNA, I installed Kodi. I don't know if it's worth mentioning, but I also installed OpenHab during the same time.
Now, the Kodi Desktop Environment is not rendered in VNC and so I had to enable 'Experimental Direct Capture Mode'. This caused my VNC CLient to say 'Cannot currently show the desktop'. To rectify this, I tried to disable the option on the Pi with my keyboard and mouse, and that brings me to the issue.
The keyboard and mouse receive power (lights work). The USB ports themselves work fine, since I'm able to connect the hard disk to any of the ports and use it without an issue. The keyboard also works without any issues on the terminal during boot. But once the Desktop GUI loads, neither the keyboard nor the mouse work. I've tried removing the hard disk, thinking it was a power issue, but that doesn't seem to be the problem. What can I do?
EDIT: This is not a duplicate of this question, since I don't get these errors:
libkmod: ERROR ../libkmod/libkmod.c 554: kmod_search_moddep: could not open moddep file '/lib/modules/3.18.5-v7+/modules.dep.bin' Error opening '/dev/input/event*': No such file or directory