I have an SSD in my MacBook (Pro 9,2; encrypted), and until recently, the apple icon appeared almost immediately after pressing the power button. Soon after that I would be able to unlock the disk using my password and then boot in ~10 seconds. A couple of days ago, I installed rEFInd on a flash drive and then booted from it as a test (I need the stick to boot into Ubuntu on my second drive and was in the process of reinstalling it). I was then in the rEFInd menu and chose one of the tiles (I think it was "Boot Linux from 16GiB FAT volume" or something like that). Naturally, since no Linux was actually installed, I was met by the black screen with the blinking cursor and powered the computer off by long-pressing the power button.
Ever since then, it takes almost 20 seconds for the Apple logo to appear after power on, even though the rEFInd stick is not connected. This triples my boot time and I see no reason why it should be so, since I did not change anything on the SSD.
Edit: The process can be shortened by pressing ALT at boot, then manually selecting the SSD, after which booting will begin immediately.
Can anybody tell me a) how to diagnose the problem and b) how to fix it?