I had the same problem after replacing a hard drive in my computer. It turns out that I couldn't update the apps because they weren't downloaded onto my hard drive after reinstalling the new one.
In iTunes, click on "Apps" in the left column. Then click on "All" in the top nav bar. See if the apps you can't update are listed. If not, find them in the store and redownload them (you shouldn't have to repay for them if you purchased them in the past with the same iTunes account). Once you've got all your apps showing in the "All" window, you should be able to update them.
It would be nice if Apple reinstalled and updated purchased apps rather than give that cryptic message. Hope that helps.