Please go to "Settings - General Settings - System - Limits". Then set all three items to max value and see if your missing albums show up.
I had similar (missing album) problem when I completely filled up my 240GB HDD 5.5G, though the problem did not occur at around 128GB. I cannot remember exactly when but it was probably at around 190GB when albums started to be missing. I fixed the problem by changing the above Rockbox settings.
Note: I have 320 Kbps mp3s instead of flac files, so I have about 3-4 times more files on my 240GB 5.5G than a typical flac only guy. That is a heavier load to the RAM of iPod.
I may be interested in buying your 256GB SD card at $115, if it pass h2testw with a computer. Please feel free to PM me.
Edited by zzffnn - 2/14/14 at 10:16am