Because of the way sage 100 processes the external command, even if you configure the external command in the bat file (or VBScript) to wait until the process finishes, your bat file will finish processing before the job does.

If you are not getting the results you expect when the job is executed via the bat file, try switching the command to use UION instead of UIOFF and either DISPLAY or MANUAL instead AUTO and then run the bat file manually. 

If you do have the bat file set up to be ran under Windows Task Scheduler, you need to make sure that whatever account it is configured to run under has all of the required NTFS permissions to access the MAS90 directory and the data source for imports or destination folder for exports.

As for your question regarding the Cycle Options, i can't say i have used it at all but it seems like you could use it if you wanted to kick off an import/export job at a certain time during the morning using Windows Task Scheduler and then configure the Cycle Options to repeat every hour for 10 cycles instead of configuring the cycles in Windows Task Scheduler.