When a repeater is powered behind a command block, the signal is not sent through to the other side properly.

In the first picture (16w41a), the signal is being transmitted normally.

In the second picture (16w42a), the signal does not go through the command block like it did before. This happens regardless of success of the command in the command block.

In the third picture (also 16w42a), it is interesting to note that when I added redstone wire after the inactive repeater, the signal suddenly went through the command block and everything seemed normal.