If padding is applied (32k sectors on), then the various sector references in the VMG_PTT_SRPT and VTS_MAT tables are altered. This is how the DVD actually reads the disc - by examining these sector references.
Oh, and even if you haven't used padding, the files can be moved if you are doing a DL disc, where the LB cell needs to end on a sector that is a multiple of 16. Just the rules of DL burning.
Please upgrade to the latest version - it's free.
Regards