I don't know wiiflow, but does "usb1" refer to the partition or the usb port?
• if it's referring to the port :
you need d2x r53 to use port1 (top port on Wii, bottom-back on WiiU).
you said you always use bottom port, so maybe wiiflow is trying to mount the wrong port and as a result you get "game not found"?
• if it's referring to the partition (which is more logic) :
seeing both Wiiflow and USBLoaderGX can't launch the game, I suspect the issue is on your HDD, not in your console's setup.
and seeing it's only some games, not all, it means it's not a HDD problem.
- Either the file is not properly named, or in the wrong folder, or you have the folder but miss the file
- Either the game is bad (corrupted, or 0byte?). verify your game is not corrupted with WiiBackupManager's Sha1 option, or with Wit if you are not on Windows.
- Either the .wbfs file is write protected. FAT32 seems to have a problem with protected files, be sure you check the file properties on your computer and disable the read only attribute.
if you installed the game manually, maybe the extension is wrong, or filename is wrong (should be TitleID.wbfs, not <Title>.wbfs)
always use wii backup manager to properly install the game (not just copy or convert)