got my old card to work again, new install took a long time. i just cloned from my old card to my new 16gb card and the system is just as fast. There is something in the files that makes the speed difference. I also notice when emulation station front end is loaded, the movements is still jerky until about a minute later. i'm guess when the emulation station is loaded i'ts still loading also.
Here is a copy of the folders. hope they helps you out. this is taken from the 45 sec boot menu.
https://www.mediafire.com/?92czbgzzgidw2pv copy of recal box folder
https://www.mediafire.com/?92czbgzzgidw2pv copy of shared files minus roms folder.
Just a hint most 32 bit game emulators do not work with the pi zero. maybe get rid of all the emulators that is not needed. Should make the system boot a bit faster