You can get a stack overflow message when you run a 16-bit apps from a command line. This is most likely to happen in batch files which recursively call the same program. Rename batch file to have a .CMD extension. Make sure that DOSONLY is not specified in CONFIG.NT and that NTCMDPROMPT is specified. This will cause the DOS subsystem to exit and reload between each and every execution of the .exe you run which should clear the stacks problem. Slower but if its broke ASIS, so what.

Tim Hill's text on command line scripting is outstanding. If you have an extensive background, writing bat files, forget it. Otherwise, get it.