I haven't yet used the utility myself but if it uses the current company that was set when SYZCON was launched then i believe you should be able to create a text file, place it somewhere under the MAS90 directory, such as MAS90\CM\Script. In the text file, you'll add a line to set the company code followed by a line to run the utility. So it should look like this.
%SYS_SS'SetCompany("ABC")
Run "..\Utility\ap_update1099s_utl"
%SYS_SS'SetCompany("ABX")
Run "..\Utility\ap_update1099s_utl"
This will only work well if the utility doesn't actually have any prompts, if it does, you'll have to babysit it as it runs each time. To kick off the text file, after launching SYZCON and once you are at the prompt, type the following making sure you use either relative or full path to the text file you created.
perform "..\CM\Script\Update1099sForMulCompanies.txt"
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David Speck II
Tennessee Software Solutions
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