I though it could be the limestone powder coming threw affecting the padsthink your on the money there mate,  i had simular problem with sores on the back end of my dogs ball bag from sitting looking out the pen gate all day.  After alot of time and trying different meds/creams i figured the mix in the concrete wasnt right,  too much lime. I used a standard garage floor/ driveway clear sealant ,  started to improve immediately,  and problem gone completely in about a week..  doesnt have to be anything too pricey,  once youve put a barrier  between lime and dog,  jobs oxo , hope that helps you