As you say that it 'ran fine' before, and only recently started to malfunction this way, it is clearly not due to a bug in uLaunchELF, but rather due to something that has happened to the content of your pendrive.
Most likely the filesystem itself has been damaged somehow, which typically happens if you remove the pendrive, or reset the PS2, during write operations. On a PC running Windows (but never on the PS2 running LaunchELF) it can also happen if you remove the pendrive when no operations are visibly going on, but without using the special 'Safe Removal' gadget in the 'system tray' (in bottom right corner of the screen). That is because Windows likes to keep some stuff in long term cache, writing it out to the drive only when you request removal. (Insane to be sure, but that's Windows for you... )
This happened to me once, when I removed the drive several minutes after copying a file to it, and after having verified that this new copy could be read back completely. Yet, when I removed the drive *without* using that safety gadget, the filesystem was damaged, and I had to reformat again.
The only thing I can recommend, is for you to use a PC to backup all the contents of your pendrive. Then reformat the pendrive, and copy those contents back again. And as always for PS2 use, make sure that your pendrive format consists of a single partition using FAT32 filesystem.
Btw: In mentioning the uLaunchELF version, please always use the full version designation. Remember that ALL uLaunchELF versions have been called something that starts wiith 'v3.41'. It is the next character, which you left out, that determines the precise version. (current version is 'v3.41t')
Best regards: dlanor