Here's what I did - instead of "zipping up" the project file, go into XCode (I'n on version 7.x), and go to PROJECT >> ARCHIVE - and archive that sucker.
It auto archives as an IPA in the proper structure.
The way I did it before was by ZIPPING it up from the FINDER app, and then changing the extension to IPA -- DONT DO THAT.
Once it's archived (from within XCode), it shows up under ORGANIZER, so go there to submit it to apple as a new build.
This was my fix after half of night of trying to submit with Application Loader and it worked fine - had a dozen other issues prior to this but each issue was knocked off the list one by one, so maybe it wouldn't have submitted had I not fixed those, but the above process submitted the first time I tried it - and that was after using Application Loader probably 15 times with no dice.