As a native San Josean, ORBX placement of downtown is fairly accurate...however as you mention there are some out of place buildings such as at threshold of 30L-eeek.
After deleting the .bgl file as suggested above: (ADEX_FTX_NCA_KSJC_Mineta_San_Jose_Intl.BGL)
In the same Iocation I also scrolled down and simply renamed the following file:
FTX_NCA_objects_KSJC_PLC.bgl
to
FTX_NCA_objects_KSJC_PLC.off
TADA! Problem solved.
***IMPORTANT: Scrolling further down you will see a file:
FTX_NCA_objects_San_Jose.bgl (DO NOT TOUCH THIS ONE)