Transfer Purchses in Itunes is not transfering applications

I recently bought a new computer. I managed to transfer everything in my itunes from the previous computer but I am having issues getting the applications that are exclusively on my iphone to transfer onto my computer. I've read all the info on how to do it but its not working. I've authorized my new computer, and I've done the "transfer purchases" and even though itunes seems to be going through the motions of transferring the applications, when the progress bar finishes there is no sign of the applications. So as of this moment my applications are the only thing not synced because when I click on the "sync applications" option, the pop up tells me that all the apps on my iphone will be cleared and replaced with the ones on my computer (which don't include the ones I've downloaded straight from the iphone).
I was so frustrated that I re synced my iphone with my old computer and tried to transfer the applications on that computer but it didn't work either!! So I am thinking this is something to do with the new itunes 9? Help!

Purchased applications can be downloaded over again, see this article for details: How to redownload purchased applications from the App Store

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