Hi,
I don´t have the VFR South-East LFTH airport but I have the Azurpoly LFTH scenery and here I have no bumps with or without the AIRACs. Have you checked, if your content-file is correct - means that you have set the correct priority for this scenery?
Are you able to upload your content.xml file that we can check this?
Normally, the scenery should overwrite our runway data when it´s set from the scenery-designer and when the package-priority is set correctly. The priority can be checked by yourself (or here by us) - if the runway-data will be overwritten, that can only be checked by the scenery-designer.