Multiple hole locations with standing features can cause undesirable results if you are trying to keep the retract height to a minimum, for time constraints.

By using just the Optimized option:

http://www.cadcamsystems.com/graphics/drill-opt.jpg

Using the Fence selection instead of picking individual holes:

http://www.cadcamsystems.com/graphics/drill-optfs.jpg

http://www.cadcamsystems.com/graphics/drill-optfsh.jpg

Just make sure you turn off the Drill Optimization as well:

http://www.cadcamsystems.com/graphics/drill-optfsho.jpg

Results are shown and if you are using very large arrays the ease of Fencing is a big time saver:

http://www.cadcamsystems.com/graphics/drill-optfshof.jpg