PLEASE someone let me know if you have a fix for this. I have a TON of highlights and bookmarks so I can't (don't really want to) delete the file. (B&N this is something you should consider saving in your next update so we don't lose everything!).
This is probably the problem, unfortunately. I can't be sure, because it hasn't been reported often for NOOKColor, but it has been repeatedly reported that heavily annotated books begin to have problems such as you describe on the e-ink NOOKs.
It's not a far jump to assume that that might be true of the NOOKColors, as well.
Maybe someone else will have a solution for you. .
Maybe try moving the trbld file then reload it from the PC. Work with that copy and see if the trbl repeats. Might be corrupt file from the site or corupt during the move from PC to Nook.
I have had a couple books flake out and one had to be deleted then repurchased(free). The other never would work.. Gave up on it cause it was a freebee
Good luck and let us know what you find