I've been having problems with this issue for a while now. I've tried re-indexing spotlight and removing a Managed Software Update program I had installed, all to no avail. iTunes will inform me there in a new update available and will direct me to the App Store, but there it does not appear. I have resorted to downloading updates manually through Apple's download page, but would really prefer to use the App Store. Does anyone have any suggestions or know of this being an common issue? Thanks for your help.