Just updated my RT-N66U. The MAC filter has been split off into 2.4ghz, and 5ghz like it was previously. This causes some issues when copying the configuration over from the previous 378.55 build. It adds the name of the Device on the end of the MAC like this AA:AA:AA:AA:AA>Name. It won't allow you to delete the entries, and adds garbage to the end after each delete, and apply attempt. To restore the configuration I did a factory reset, then used the NVRAM save and restore tool from these forums. I also tried restoring from the UI, which gave the same results.
I had the same issue.
Solution:
1) backup macfilter in ASCII format (TXT)
2) activate ssh daemon
3) login
4) nvram show| grep maclist
5) clear all macfilters for all wlan interaces ("nvram set wl[|0|1]_maclist[|_x]=")
6) nvram commit
7) reenter all required macfilters from GUI