I finally found out what was wrong with FDS. When fixing regressions happened between 0.122 and 0.123, we lost the emulation of the 32KB RAM adapter and we ended up directing all writes to (a copy of) the disk itself, corrupting the subsequent reads...
fixing this bug, we now have many more games which load fine (as they did e.g. in 0.117 and 0.122), instead of returning disk errors. Among the others
(in order: Apple Town Monogatari, Aki to Tsukasa no Fushigi no Kabe, Eggerland and Akumajo Dracula)
There are still some SRAM issues, tough, and as a result some games fail to start as they should (notably Zelda and Zelda 2, and Metroid). I'm not sure if the latter games have ever worked in MESS, but I would definitely like to fix them as well