A small flaw has been discovered in the current implementation of disorder masking when it is combined with masking upper or lower case residues (
casemask=X dismask=T). Rather than predicting disorder on the unmasked sequence and then combining with any case masking, disorder predictions are currently made on the masked sequences.
Hopefully, this will have minimal impact for the majority of cases. (Although I am not certain, I suspect that it will produce a tendency to over-predict disorder and thus under-mask.) This bug has been fixed for the next release of SLiMSuite. Note that other masking combinations are not affected.