I believe this may be an error on Apple's server end. I've run into the same situation last night (4/9/14) and this morning. I've been running Xcode 5.1 for a while now and have uploaded other IAP content packages with no problems over the past few months.
/usr/libexec/productutil doesn't appear to have a way to check the version, at least no way that I can find. I've even tried installing the latest Xcode GM seed (5.1.1) but that didn't help.
I've submitted an inquiry to Apple support. I'll report back if I get an answer.