In that case I think the important part to note is that the "eUpgrade available" message on the website is directly linked to the price displayed on the website for sale at that time, and not necessarily to any other bookings made at a different price point. Obviously there's the caveat that it's not always right, but I think we can assume that while AC doesn't want to reveal many details of when/why/how fares become instantly upgrade-able, the message on the website isn't meant to be intentionally misleading.

To answer your question though, whether anyone has seen this before, the answer for me is yes, plenty of times. Though I mostly see the opposite of what you're seeing where the website says no upgrade is available for Latitude, but my Lat FP will immediately confirm an upgrade. I have seen what you're seeing though, where my Lat FP won't upgrade even though the fare offered on the website says it will upgrade.