Copied from: http://mod-buildcraft.com/forums/index.php?topic=6.0 (lolkingfred)

When an item with a damage value is placed on the hot bar left of a Buildcraft pipe, the icon loses its transparency. This only happens when items without a damage value are absent. See the video below for clarification.
http://youtu.be/S2M3t-2GGss

At the end of the video you can see the pipes turn opaque.

...the issue was on the forums for a reason.

Do not open an issue if you're not planning to fix it, intead open a thread on http://mod-buildcraft.com/forums/index.php?board=2.0

This might be a bug in vanilla.

@czaftan - given your other post, I'm assuming that you're interested in working on this bug, is that correct? In which case, I'm keeping this one open and added you to the list of "external contributors". You will still need to submit a pull request, but we know who to bug to know more ;-)

Ups. I deleted my comment by mistake. The comment says that I'm going to take a look on this bug. Sorry for misunderstanding.