Thanks for this observation. I tested my fives and confirm this problem (using Klipsch Connect iOS app). The EQ settings are not stored on speakers and prior every use I have to use the app to re-select my custom EQ to cancel the boomy bass away. When the app says "Getting latest info" it skips the EQ settings. It will show the last user selected setting but in reality it has defaulted to "Flat" -setting (which in fact is not very flat at all). So the app gives you a false indicator.
I think Klipsch made a good job featurewise with the new update, but a little more time spent on quality control would have paid off. I expect this bug to be fixed in the near future.