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The only problem that I've had was on the 1.2 NOOK firmware, where if I transferred to the added microSD card, I had to turn NOOK off (white screen) and back on to get it to rescan the added card. I haven't had any problem since 1.3 came out.
So I'm shooting in the dark here.
First, I assume that you're using either a NOOK 3G or NOOK Wi-Fi with 1.5 software. Right?
Are these going onto the main card, or onto the microSD? If onto the main card, are they going into the 'my documents' folder or somewhere else?
Have you tried a power-off and power-on? That should restart all of the reading software.
Have you tried a full re-boot (not factory fallback): hold power button for 20 seconds and turn back on, once? That should restart Android as well as the reading software.
How many e-books have you added? NOOK was, at least in the past, reportedly limited to how many entries you could have in each folder (somewhere between 1000 and 1500). Putting the e-books into folders within folders helps. I think think that's why the NOOK plugin for Calibre was changed to put the e-book and its cover JPEG into a folder--that cut the number of entries in the root folder in half.
Is it plausible that there's a "bad e-book" in there? NOOK displays everything by author and title, and if an e-book is missing either of those fields, NOOK can get cranky. You'd probably have noticed that in Calibre, though.
There's no reason that Calibre would do this, so it'd be something you'd be doing yourself: NOOK reportedly has trouble if you rename e-books on the device itself (as opposed to deleting the old file and copying in one with the new name). Still, a Check for New Content should clear that up and you've done that.
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