In my Android's (4.1.2) built-in calendar app, in its settings, there an option: "Use home time zone" ("Displays calendars and event times to your home time zone when traveling").
I have it check-marked. What it allows me is that if I have scheduled some meeting at 10am for the date I will be in a different time zone, if I didn't have that, - it would be showing me the event at a completely different time.
However, when I am already in a different time zone, setting new events can mix things up. The event reminders then happen at a wrong time, not when I expect. (I forgot the exact details.)
Why am I writing this? I suspect that you may have a similar effect. So, you can check what that option is set to on your phone, and then toggle that setting and see how the behavior will change. Maybe what you are observing is the peculiarity of your calendar program, and not that of Aquamail?
(Just in case: While using the built-in calendar app, I am using Google calendar, not the internal device calendar.)