Your mention of trigger not working with Tasker 4.6 had me worried enough to check.
I also have 4.6u3.
After creating an "AquaMail plugin" action in Tasker, and setting it to "check mail in All accounts", I'm able to trigger it "by hand" using the "Play" button, lower left, in Tasker's "Task Edit" window -- and it makes Aqua check mail in all accounts.
So maybe the problem with 4.6 is with this Tasker task not getting triggered, on that end, and not with Aqua?