I hooked up an aux switch to an H9 with the latest software on it, and I assigned it to the tap tempo function. Everything worked as expected. The aux switch changed the tempo when tempo mode was on and when it was off. So, I'm not 100% sure why you're having the trouble you're having.
If I were you I'd try resetting the H9's system settings. Sometimes the system settings can get messed up after updating, and it can behave strangely. You can do this by turning it off and then turning it on again with the right footswitch and the HotKnob switch pressed (this switch in the upper left hand corner of the H9). After you do this you'll need to reconfigure the aux switch settings in H9 Control again.
If this doesn't help, there's a function in the latest version of H9 Control that will record your H9s settings so that you can send them to us to look at. You get to this by pressing the Pedal button in the bottom menubar in H9 Control, then pressing General Settings, and then going to the 'Capture System Settings' page. You can export your H9's system settings there, and send them to support@eventide.com for us to look at. But please try resetting your H9s settings first as I described above to see if that helps.
