Big %-age of cracks, menu disks is done very unprofessional, with dirty code, what easily fails on some other TOS version, with different RAM amount in machine than 'developer' had. And Automation was probably 'leader' in this
So, what TOS version, what Atari model you have ? How much RAM ?
Of course, it is possible too, that floppy emulation of CE is still not good enough. If you can, try those problematic images in some emulator - Steem, Hatari, where can set RAM size, using any TOS version - and then we will know better what is the real problem.