I've found that comparators will not update the output from a chest block if the connected chest block gets broken and items drop with it.

Steps to create problem.

1. Set up double chest (regular or trapped).
2. Place comparator facing out the back of the right-side half of the double chest. (Not the left one, as breaking the right box leaves all the inv in the left box.)
3. Place a stack of items in the double chest. (Comparator lights up.)
4. Break the left box, and get your stack of items. (Comparator stays lit, though it shouldn't because you have your stack of items.)
5. Open the box, and find nothing inside. (Comparator is now turned off.