Hi there Steven,
I have mostly resolved this now..
It appears that it was the Pasti plugin which was preventing those Stonish MSA files from opening in Steem SSE (now I'm using SSE 3.9.1). I was using Pasti 0.2j, it would seem that removing the DLL and later re-adding has allowed Steem SSE to open those Stonish MSA files for Lemmings 21, 22, 44, 45. Very very odd, but now working.
As for the TOSEC .ST files for Lemmings 21, 22, 44, 45 - these appear to be damaged in some way.
As a test, I used MSA 1.41 to write the Stonish .MSA files for these disks out to blank floppy disks under emulation, this has worked and I now have 4 working .ST files for those particular disks - all games tested from each disk, inluding the Lemmings file checkers on 44 + 45. MSA-II and JayMSA seemed to write out the Stonish .MSA files incorrectly to the disk drive resulting in broken .ST files.
Below is the info regarding these particular disks, comparing the TOSEC .ST versions to my new MSA 1.41 produced versions, I think these are the only disks affected - Filename, CRC-32, Size:
Lemmings Menu 21 (19xx)(Lemmings).st
Lemmings Menu 22 (19xx)(Lemmings).st
Lemmings Menu 44 (19xx)(Lemmings).st
Lemmings Menu 45 (19xx)(Lemmings).st
So I suppose these particular TOSEC disks may just need replacing.
As for MSA Converter, for some reason it will not open the Stonish .MSA disks for Lemmings 21, 22, 44, 45 - perhaps they use a compression scheme it does not support or something.