Does anyone know what this means when IRS processed an amendment but hasn't approved the original that I made the amendment for?

You will need to reach out directly to the IRS for more details.  The below instructions will help you get through their phone system a bit quicker.  

IRS: 800-829-1040  

Hours: 7:00 AM - 7:00 PM (local time zone)

Monday-Friday

• Listen to each menu before making the selection.
• First, choose your language. Press 1 for English.
• Then do NOT choose the first choice re: "Refund", or it will send you to an automated phone line.
• Instead, press 2 for "personal income tax".
• Then press 1 for "form, tax history, or payment".
• Then press 3 "for all other questions."
• Then press 2 "for all other questions."  It should then transfer you to an agent.

Or, you can visit your local IRS Office. 

Thanks HeatherPLO,

I got letter 5071c from IRS today and needed to verify my identity with them. I have no idea why I was flagged (they didn't know either) and I wish they contacted me sooner as it has been over a month since I submitted my return. So, hopefully it will go smoothly from here. They told me it may take another 9 weeks...

Thanks again,

Isao

Thanks for the update.  For your reference, I am including a resource that provides tips for handling identity verification.