Chaos Strikes Back for Atari ST doesn't work very well with emulators. Here is some information for WinSTon v0.5 emulation:
If you use the Automation Disk 192 found at Little Green Desktop, you won't be able to load your saved games because of a crash. The archive on this site contains a working version of the Automation Disk 192. However, you will have to insert the disk image in both A: and B: drives.
If sometimes the mouse gets inverted vertically, it means your disk image is infected by an Atari ST virus called "Ghost Virus A". The disk image on this site was cleaned with the Ultimate Virus Killer 2000 anti-virus.
If you use the other version available on this site (MSA format images), you won't be able to save your game.
Consider using the Amiga version (which has better graphics and introduction than the Atari ST version) until newer versions of emulators appear and things get better.