I have this setup:
http://imgur.com/n8CbKg4

The filter has flax seeds in it and this entire thing is hooked up to my flax farm. Every once in a while, I notice flax seeds in the string chest. Is this intended? IMO its a bug...

If it is intended, how do I fix it?

Kinda intended. When two seeds are going into the Filter in rapid succession, the first seed going in locks the filter for a moment until the first seed gets shot out of the back. This is because the seed first must go through an internal buffer. Though I think I can solve it, by first seeing if the buffer is empty and trying to inject the item right away. Fix coming up.