Reddit mentions of Toshiba Canvio Connect II 1TB Portable External Hard Drive 2.5 Inch USB 3.0 - White - HDTC810EW3AA

FCE Ultra GX and Snes9x GX both did have some new versions developed that I myself had to adapt to the changes of once I discovered them, the biggest visual one being the vertical split with the ROM list on the left and space for screenshots and covers on the right.

You may want to consider backing up and removing the folders for each respective emulator on the root of the SD card to see if some settings file might be interfering somehow; basically do a clean copy of each emulator, then add ROMs and saves back to the appropriate places.

I have the cIOS's from the guide and rips work fine for me, so I suspect something has either gone wrong with your setup or GX doesn't like the device you're using. It doesn't matter if your USB drive is new, flash drives generally aren't recommended anyway, and there's no assurances that anything is guaranteed to work.
This is all basically unofficial hacking after all.

Powered drives tend to work better, but again, no promises on what will or won't work. I got lucky and took a chance buying this drive that works fine for me without a y-cable formatted to FAT32 32-bit clusters, and I bought another when I homebrewed a friend's Wii later.