I noticed an issue with the indexer and BeeSink as well...

UPDATE: I noticed that this only happens when there isn't a bee in the indexer... As soon as you add one bee to the indexer the BeeSink connects and works.

Setup:
I was trying to setup 1 indexer for princesses and queens, a 2nd indexer for purebreds, and a third indexer for the remaining bees.

The 1st indexer connects and can even be sent bees, but when I placed the 2nd and 3rd indexers the BeeSinks wouldn't connect (Screenshot below). I moved the setup to the center of my area and the BeeSink wouldn't connect to any face of the indexer (either by moving the BeeSink & piping from one side to another or moving the indexer).

Forestry 2.3.1.1
Binnie Core (Extra Bees, Extra Trees) 1.8.0
Logistics Pipes 0.7.4.dev.151

Do other BC pipes connect to the indexers?

The indexer piping connection works as long as a bee has been (manually) placed in the indexers' inventory. After the bee has been added it can be removed (leaving the indexer empty) and the piping will continue to work.

I don't remember any issues with vanilla BC pipes but will have to check when I get off work.

Ok, See attached screenshots... If the indexer is placed and piped before a bee is inserted no pipes connect, after a bee has been placed in the inventory (even for a second) any pipe BC/LP will connect.

No bee added:

Bee Added & removed, then piped

Version info:

If BC pipes also don't connect then I suspect it's a problem with the Indexer. I think that for some reason it says it has an Inventory Size of 0 when there is no item inside the indexer itself.

try update to newset verison to see if the bug have been fixed

@SinusoidalC - Aye Aye!

As of LogisticsPipes 0.7.4.dev.205 for mc 1.6.4 BeeSinks still will not connect to an empty indexer. Connection completes when any bee is added to the indexer manually.