Hello!
Are all 4 of the USB ports on your Wii U being used?
Most people , or at least it is recommended, have two separate hard drives for the Wii U and the vWii.
1 dedicated for Wii U content, 1 for vWii along with the SDCard required to load apps.
I am not sure if USB Loader GX Supports loading games from the SD Card, if you can select that somewhere. I do know that you are absolutely required to put all Wii Games in the WBFS folder on the root of the drive.
Make sure that your wii games are installed to a WBFS folder at the root of the SDCard, regardless for the time being for troubleshooting's sake.
You can customize the paths in WiiFlow to point to wherever you put the Wii Games on your sd card. Just make sure you set them up in the paths.
I will go ahead and tell you that you may need to try beta52 instead of beta53-alt as you have it.
Beta52 is seems to be more compatible with older hard drives, sd cards, and just weird scenarios where you are trying to do something odd with one of the loaders.
Beta 53-alt is nice as it provides for multiple usb support so its great if you can get everything set up and working, but unfortunately if something isn't working for you... Try and go back to beta52 and see if it works.
Also, you do not need to install ALL of the slots. Off the top of my head, I don't even remember what 250 and 251 are used for. 249 is the core one you are going to point all of the loaders to.
In fact, if you try beta52 and still have issues. Go into each loader and specify that the IOS you want to load is 249. Both are set to auto by default.
I have noticed that by specifying the IOS desired, it can get around some weird quirks.
Now what I would highly recommend is you not to do what you are doing. I would highly recommend, in my own personal opinion which might actually be a bad idea, is to have separate hard drives for each mode and an SD card for your apps and other settings. Have your high capacity games loading from your hard drive and the small apps or loaders on your SD Card.
You can use a Y cable for both the front and back USB ports. There are 4 total. Plug in the vWii Hard drive to the back ports (for maximum compatibility when the loaders are trying to scan for where your hard drive is). Plug in the Wii U hard drive to the front ports.
You will get annoyed with having to unplug the vWii hard drive cable when booting into Wii U mode, but you don't have to unplug the 2 usb plugs. Just unplug the part that goes into the hard drive, leave the 2 usb cables plugged into the back.
If you need to recharge a Wii U Pro Controller, you can unplug one of the vWii USB plugs when you are in Wii U mode since the vWii Drive isn't being used in that mode anyway. If recharging in vWii Mode, unplug one of the Wii U Hard drive usb plugs as the Wii U hard drive wouldn't be used in that mode.
You can stealth the drive you would use with the vWii, but then you have to worry about each individual loader being compatible with this change... I found it just easier to take the 2 seconds to unplug the cable instead of worry about loader problems.
I do realize that my recommendation does not solve your issue, but it is something that you can think about in the future.
Right now you go back and write beta-52 and then see if things load. If they don't, make sure you have specified the Wii Game path in WiiFlow.
After path changes and such in WiiFlow, always press the Home Button on your controller and select reload cache. Get used to that, its important!
If you still get nothing, try specifying IOS 249 as the IOS you want to use and restart WiiFlow and then reload cache.
This should work, if it doesn't then there might be something else going on. But I am sure this will work for you, must think positive.
The Wii U can detect negativity and frustration, if you stay positive then things start to magically work...
Hope this helps and have a great day.
Edit: Oh and just as a general note, and this may not even apply at the moment but it is something weird to remember about the Wii U and USB hard drives...
If you find that your drive isn't getting detected, whether you have it plugged in the front USBs or the back USBs, try swapping your Y-Cable's usb plugs around. Unplug each from the ports and swap the plugs.
I don't mean take the plugs and plug it from the back and into the front or front and into the back, I mean just swap the two plugs from wherever they are currently plugged into around. For example in the back, unplug the Y cable's 2 usb plugs from the back and swap where they were plugged in. They aren't specifically labeled USB PORT 0, USB PORT 1. So it is hard to know which is which. But just swap the plugs around and try to see if the hard drive gets picked up afterwards.
Same with the front as well. Often times just swapping the plugs around results in a drive getting recognized, whether it be that the data+power plug wasn't getting recognized or the power only plug wasn't getting enough power. Who knows...
It is hard to explain this since they aren't labeled, instead of saying swap the USB plugged in port 0 with 1 and 1 with 0 in the back. But I think you get what I mean.
I really wish nintendo allowed you to upgrade the internal memory. You may be wondering why you can't, that is because there isn't a hard drive inside. It is solid state memory on-board. I guess we should be thankful they at least put that in the Wii U instead of forcing everyone to buy hard drives by default.
32GB is just not enough for the Wii U.