Here's how I eventually resolved the issue.
Despite being told multiple times by US CBP and CBSA (I have Nexus) officers that my profile looked fine in their system, I contacted CBP through their website and explained the issue hoping someone more familiar with the technical intricacies of GE would take a look. I received the response below:
It seems that you had multiple kiosk uses during a single reentry on 01-04-2015. When multiple kiosks are used, fingerprint data is deleted from the GOES profile as a security feature. To resolve this issue, you will need to visit an enrollment center to have your fingerprints captured and saved into your GOES profile. You may visit any airport enrollment center on a walk-in basis. Please ensure you use only one kiosk upon a reentry into the United States.
It is our goal to provide you the best information we have in response to your question. If you follow the information provided in our response, and still need assistance, please reply to this email and we will investigate how we may further assist you.
Thank you again for contacting the CBP Information Center.
Sincerely,
CBP Information Center
So despite being told over and over again that my profile was fine, my fingerprints were actually not there. Even when I went to the enrollment centre at LAX, the officer at first refused saying my fingerprints were already in the system until I showed him that email on my phone. Since having them re-captured, everything has been fine.