I have this debilitating issue with my Macbook pro 2014 retina, it has this long delay before the apple logo shows up - somewhere between 40 to 60 seconds. I've tried all the usual tricks multiple times, NVRAM and CMS reset, permissions repair, reinstalled a fresh OS X Yosemite twice. The machine is running on an apple 128gb SSD. So, new freshly installed system, very first boot, apple logo appears almost instantly. No problem. As I open a few windows, particularly the 'startup disk' in the preference panes (but not doing anything else but clicking on it), the long delay appears at the next startup. I run 'permission repair' on the drive and at this very early stage, it might fix it but only momentarily. However, without exception, once I plug any peripherals in - usb drives, memory cards etc., the fault is back. And I don't mean leaving it plugged in through the startup, only connecting it just to copy a few files. Then, after a few startups, nothing will fix the delay anymore. It's almost as if the machine is extremely sensitive to connecting of new drives, bootable or not, even if only momentarily, and throws the boot sequence out. Other glitches I have observed are also related to boot. I make an Yosemite installer with Diskmaker X and it shows on the startup disks pane, but will NOT show up at startup boot manager with the option key pressed. If I make same installer through terminal, situation is reversed: it will NOT show up in startup disks but will appear in boot manager. These symptoms might not make much sense but there's definitely a root cause of all this, and I think it's fair to say the process by which the machine recognises eligible boot drives is partially corrupt. In fairness, it always boots in the end but seems to be terribly hesitating. I would also assume it's something that resides outside of the operating system, because multiple fresh installs didn't fix the issue, and after the logo appears everything boots lightning fast. Sorry for the novel, I'm out of ideas at this point, and any advice would be greatly appreciated. P.S. Checked to console log, there is no activity whatsoever recorded within those 40-60 seconds. Did the hardware test, came up with 'Potential display problem' (code VFD002). I'm reluctant to think this is related.