I have experienced the same problem today.
I have 3 SD card and I wanted to clean up the mess in them, so I copied all the files to PC hard disk, reorganized them and then reformatted the cards to copy back the files. While doing the copy into the SD I have not copied the _DS_MENU.SYS, to leave the R4 to recreate it. But I got this problem and in all the 3 cards! My kernel is 1.17. But I remember to have seen it also on a previous version. Last time it was due to the fact that I upgraded the kernel on the SD, but I have not removed the old _DS_MENU.SYS file.
To fix the problem I removed all the files related to the kernel and reinstalled it using files from the original archive.
There was more than 60M of free space on the SD cards, so I do not think it was related to free disk space.
I wondering if the problem could be in the microSd adapter included with the R4, since I used it to copy files from SD to PC /PC to SD. The SD cards are from different brands (Sandisk and Kingston) and never experienced problems with corruption in ROMs, savefiles. I have copied the kernel files from SD to PC and then back to SD (after the reorganization) and these were working correctly before. The _DS_MENU.SYS was recreated, so this should be something related to curruption of the other kernel files. But, I turned off/on the DS 5/6 times after I have experienced the problem the first time and in 1/2 cases it was working correctly! A bug in the kernel?