BO3 are not pasted correctly.
Example for a BO hiccup, this cemetary:
http://s24.postimg.org/qd247ucxx/cemetery_good.png

When pasted looks like this:
http://s13.postimg.org/rhq623h4n/cemetery_bad.png

The BO3 file was created with BO3Tools on WorldEdit selection, and then manually edited for BlockChecks and manually placing air blocks where needed:
http://paste.ubuntu.com/5663772/

I can also see two torches falling down (always the same two torches) but I can't reproduce the other bug...

Just saw this CraftBukkit commit: Bukkit/CraftBukkit@7fd3e34. Maybe it fixes the torches popping off bug. I haven't tested it yet.

If you want to test the above fix, here is a compiled build.

This fix was included in TC 2.4.12, it seems to work fine. If not please leave a message here.