Why does my calendar no longer hold two different time alert? What I put in my second alert will change my first alert to match what I put for my second alert.
It appears that the second alert must occur before the first alert does, otherwise iOS will set the second alert to match the first alert. So, make sure your first alert ("Alert") is set to the time closest to the event, and the second alert is set to whatever time you want that is before the first alert.
On my iPhone 6s, before I upgraded to iOS 9, the Calendar alerts worked in the reverse of the way they seem to now; "Alert" had to be earlier than "Second Alert" when both are set to something other than "None". I reported this to Apple but now on iOS 9.3 there is still no change. So I created a bogus appointment for a test; if I set "Alert" to say 5 minutes before, and "Second Alert" to 15 minutes, what would occur? Firstly, it accepted these entries instead of trying to reset one alert to the same value as the other. Secondly, I got the first alert 15 minutes before the appointment time, and the final alert 5 minutes before. My conclusion: For whatever reason, Apple has changed (reversed) the way the alerts function. I find it more counterintuitive and confusing; I don't like it but at least I can work with it.
Mine had the same problem - second alert would not even show up. I had to go into iCloud and enter an email address other than outlook or hotmail. Once I added in my gmail account the second alert option became available. Apparently having the calendar linked to only an outlook/hotmail account does not allow for the second alert on the Calendar appointments.