OS X takes long to boot after starting rEFInd once

Question

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?

Answer 1

Turns out resetting PRAM and NVRAM via pressing ⌘+⌥+P+R at boot (before the gray screen appears; hold until computer restarts and the startup chime has been heard twice) fixes the problem.

I have since successfully booted both OSX and Ubuntu via rEFInd without any excessive waiting.

Answer 2

I had this happen with rEFInd before. I think rEFInd boatloader ended up in your efi partition. The excruciating long wait is rEFInd checking every device/partition to see if it's bootable.

I have the debug menu in disk utility enabled, so I just selected show all partitions, mounted the efi partition from available partitions in the top left window, and removed rEFInd's .efi file. I also emptied the trash just to be sure.

To enable disk utility debug menu open terminal and run "defaults write com.apple.DiskUtility DUDebugMenuEnabled 1". rEFInd should have is own folder, so not delete anything from the apple folder or anything else for that matter. Unmount efi partition when finished.

Hope this helps.