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Hi,
I'm having the same problem. Bought my Z3 from a Sony store just last Saturday (Oct.17) and when I tried registering my IMEI yesterday I got the message "The IMEI is not valid". I've already sent an email to Sony Xperia Contact Center and am still waiting for their reply.
Me too says "Not valid IMEI format" copied from the tag under the SD card. What gives? 
@emk wrote:
Settings > about phone >status
See if the software recognizes the IMEI
The software recognizes the IMEI, and I've received a reply from the Sony Xperia Contact Center that the IMEI is indeed authentic and registered. I guess my question now is how do I input my IMEI in my Sony account as it still says that "The IMEI is not valid."?
@uliwooly wrote:What did your Local support said?
This was the response I got:
"Thank you for contacting Sony Xperia Support. We are happy that you are using Xperia Z3. We value the importance of your concern and we are here to assist you. In response to your query regarding how to register the IMEI to your Sony account (My Support), currently Philippines is not included in the list of the supported countries."
From that response I assumed that there is really no way (for now) to registed my IMEI to my Sony account, though it's good to know that my IMEI is authentic and registered to Sony.