Your mos devices have been extracted as generic devices. Hence source and drain pins will not be automatically permuted. VXL layout pin permutation is not related to Assura LVS, hence it will not resolve the problem. You can resolve the problem as follows:
a. In Assura LVS form, go to "avCompareRules"
b. Select "Network"
c. Select "swapPins" and add the following expression for schematic side:
swapPins("pfet(Generic)" "(p S D)")
d. Run LVS