Ended up adding the commands to the lisp routine in lieu of calling the script files as Allan suggested and it works fine now. Thanks you all for your help!
;;==========================================================
(if (member "Site Plan" layers2load)
(command "-layer"
"on" "0,*|0,*DEFPOINTS,*A-COMN-*,*S-COMN-*,*S-SITE-*,*P-*TOB*,*MAIN*FH*
*FEMA*,*PROPERTY*,*LANDLINE*,*WETLAND*,*SAFE*UPLAND*"
"C" "1" "*MAIN*FH*"
"C" "252" "*D-*P-*POND*TOB*"
"C" "81" "*S-SITE*P-*TREE* LW 0.50 *S-*P-*TREE*"
"C" "74" "*S-SITE*P-*SHRUB* LW 0.35 *S-*P-*SHRUB*"
"")
)