[Nook HD, HD+ General] fizzguy:
Alternate procedure is the key to booting from SD in my experience

Your alternate procedure may be the key, if my experiences are any indication. My setup is a new HD+ (stock, not rooted), two Sandisk sdcards, one 16Gb and one 32GB (both class 4), and a Windows Vista laptop (ASUS M50S, which has an integrated SD card reader). I used SDFormatter v4.0, Mini-Tool Partition Wizard 8, and Roadkil's Disk Image, all free. The zip and rar files are attached to leapinlar's original post in this [CWM/ROOT/EXTRAS] thread: http://xdaforums.com/showthread.php?t=2062613 .

First I used Roadkil's imager to write verygreen's "sdcard-cwm-early4.img" to the 32GB SD, then tried to boot from it. After trying (and failing) to boot this a couple of times, I decided to try the 16GB instead, since my impression was other people have had better luck with 16's. I prepared the SD with Roadkil's imager as before. It took at least six boot attempts (apparently I have one of those Nooks...) before it booted from SD -- apparently persistence does pay off.

Then I found leapinlar's thread (referenced above) and decided to try some mods to the stock ROM. Since I only had the two SDs, the 16 would be the backup with "NookHDplus-bootable-CWM-6028-for-stock..." used for CWM. HOWEVER -- and this is crucial I think -- rather than using Roadkil's imager I used SDFormatter + Mini-Tool Partition Wizard to prepare the 16, then copied the five bootfiles from "NookHDplus-bootable-CWM-6028-for-stock-BOOTFILES-r4-(05.15.13).rar" (attached to leapinlar's post in the ref'd thread). I used the default format options: quick format, format size adjustment off.

I powered on, and it booted to SD the first time. In fact, after backing up, I booted to the same SD several times in a row, all with no problems. Interesting...

Next was the 32, since the 16 was the backup. I went through the same SDFormatter + Partition Wizard + CWM bootfiles as before, plus zips for a couple of mods to stock. Again, it booted from SD the first time. In fact, I have booted from it a number of times now, and have never had it boot to stock like happened when I gave the 32 (and the 16) the "Roadkil treatment". Even more interesting...

This was intringuing enough that I decided to do a few more investigations. Instead of using the files in "NookHDplus-bootable-CWM-6028-for-stock-BOOTFILES-r4-(05.15.13).rar", I used Roadkil's imager to flash "NookHDplus-bootable-CWM-6028-for-stock-4GB-rev4-(05.15.13)" to the 32, since presumably the boot and CWM code are the same in both cases. The next 10 or so boot attempts weren't successful. I was going to keep trying, but gave up when something happened and my Nook did a hard reset -- my backup SD came in handy sooner than I thought it would! The backup booted correctly the first time, but then again it was formatted by SDFormatter.

Next I reformatted the 32 with SDFormatter and added the bootfiles again. The Nook booted correctly to it the first time. The next few boots were similarly successful.

So let's take as a working assumption that, on my HD+ at least, the method of formatting the SD is crucial to whether the Nook boots reliably from it. The fact that this seems to be mostly an issue with newer Nooks isn't totally strange, because the developers of the SD reader on the HD+ may have made an engineering change because the readers for the older HD+ were too forgiving of spurious memory errors, for example. (Although that doesn't really explain why it boots correctly sometimes rather than never at all, nor why the SD is readable once the Nook boots. Maybe the boot driver is just more finicky than the driver that's loaded with the OS?)

If the method of formatting is indeed crucial, as it certainly was in my case, then the next question is whether the key difference lies in SDFormatter or Partition Wizard (which is just used to set the "active partition" flag). To test this, I used Roadkil's imager to rewrite CWM 4GB to the 32, then rebooted. As before, the boot from SD failed (I tried booting twice), but at least we're back to the flaky behavior. Reinserting the 32 into my laptop, Partition Wizard reported the primary (and only) partition as active, as expected. I set the partition to inactive, updated the SD, then reset it to active again. The purpose of this exercise was to verify that there was no spurious side effect when setting the partition status which might change the behavior at boot time. Totally unsurprisingly, this test gave identical results as before -- the Nook wouldn't boot from SD, at least within a couple of attempts. After reformatting again with SDFormatter, it booted from SD the first time. There is definitely a behavioral pattern -- when SDFormatter was used, I never encountered a boot failure from either the 16 or the 32. On the other hand, I never did get a successful boot on the 32 when prepared by Roadkil's imager.

The last thing I'd like to try, but can't without help from verygreen (or maybe you could help, leapinlar), is to format the 32 with SDFormatter, give it the same three partitions as verygreen did in cwm early7.1 for sdcard, add all the bootfiles from early7.1, and see if my Nook boots reliably. I also wonder if others with newer HD+ that don't readily boot from SD can reproduce my experience, maybe even with SD cards from other manufacturers besides Sandisk. It's kind of hard to imagine that my Nook is somehow unique, but who knows...