Well, as soon as I asked for "more meaningfull error messages", I got the following email from Apple:
{quote}
Thank you for your recent binary submission to the App Store. Unfortunately we discovered an issue with your binary that you will need to correct in order for your application to proceed to the review stage. The specific issue is outlined below:
Attempting to Change Bundle Identifier - Once a version of your application has been made available for sale on the store, you must use the same bundle identifier (as specified via the key CFBundleIdentifier in the bundle's Info.plist file) for all updates to that application; any bundle uploaded for that application that has a different bundle identifier will fail validation and not go live for sale. For more information about bundle identifiers, the CFBundleIdentifier key, and the Info.plist file, see Apple's Runtime Configuration Guidelines at
http://developer.apple.com/documentation/MacOSX/Conceptual/BPRuntimeConfig/BPRun timeConfig.html
{quote}
So I guess my initial question has been answered, and the answer is the "Waiting for Upload" means that SOMETHING IS WRONG WITH YOUR UPLOAD, and hopefully Apple are going to look at it at some some stage and send you an email explaining what is wrong. However, my status did not change, so if they forget to send this email, you could be out of luck.
Anyway, IT WORKED!!! My App update is now "in review".
*The problem was that my initial submission had a bundle id of "com.yourcompany.CheckWord", but the new one was only "checkword"*. I'm not sure when or how this changed. But all I did was edit it in info.plist (or the Target Info - Properties - Identifier, which edits the same thing).
I then went through the dance of deleting the code signing identity, build-clean all, restore the code sign identity (which should make the correct Provisioning profile pop up in the field below if you got it right), and then build, zip, upload. After about 5 minutes I checked it and it was "In Review"
Yay, soon the world will be able to make anagrams on their iPhone.