Supports not put in all needed places in MakerWare

[shingabiss]

I am rotating this object so the long protruding cylinder faces upward. I specify supports but on the preview all the supports I see are around the little opening and when I print the inset back is all saggy due due to this. I have been using the Makerware/Makerbot for a few years now and have had very good luck with most things but this just doesn't make any sense to me. I've even built in my own supports and print previewed with no supports and the program does weird things with it and removes most of them. The inset back is made using the "offset" tool inward and push pull in .125". Any ideas?