To do this you would edit the ldappl3.template file which controls the file extensions. There is a clearly marked section.
Enabling an extension does not mean all .sys files will be scanned because the default mode is 'Listed'. So if there are 30 .sys files then once you have edited and published the ldappl3.template file (using the make available to clients button in Manage Software List), then you can add the .sys files specifically in that same Manage Software List window.
LANDesk cannot do a *.sys scan on a certain directory.
Hope this makes sense.
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