I'm not sure myself, maybe someone else knows? I'm using Tiramisu too but not having the issue. You could try reinstalling Tiramisu in its entirety, I guess.
Is it possible the SD card has a problem somehow? If you formatted it for use with Wii U, what did you use to format it?
I ask because when I used an app not intended for formatting SD cards, it worked perfectly for everything with only one exception, which was a single Wii game that would not run in WiiFlow. None of the files had any issues at all, copied directly to another SD card it worked perfectly, but something in how that formatter worked created an issue that seemingly affected exclusively 1 thing, and if not for that game not running I probably never would've realized the SD card had an issue at all.
Other than that, or trying to reinstall Tiramisu, I have no ideas. If you have an extra SD card you're not using, you can test that to see if the same files work on that one.