The use of hex instead of decimal values for side_id elements results in all side id being 0. Formatting the side_id values as decimal fixes the issue.
DiskLayout_FLEX_DSDD_40T_356KB_PADDED.xml
DiskLayout_FLEX_DSDD_40T_356KB.xml
DiskLayout_FLEX_DSDD_80T_716KB_PADDED.xml
DiskLayout_FLEX_DSDD_80T_716KB.xml
A cli workaround is to specify a corrected copy of a layout file using the "-uselayout:" option. The gui may have a similar option.
The disk layout parser in xml_disk.c for SIDEID_SECTOR uses atoi() to convert the value, returning 0 for "0x" prefixed strings.