Hi Chas
What I would suggest is not to use a custom pipeline in the receive location, you could subscribe the message into and orchestration and then call both the pipelines in that orchestration to do further processing. Else you can have two orchestrations that subscribe to this message and call the individual pipelines in each of the orchestration.
If you still are bent on using the pipelines on the receive locations, then there is another thing that you can do (I would not recommend it though). You can have two send ports that subscribe to this incoming message (which will of course use a passthrough pipeline) and have them output it to two different locations, from where you can get them into BizTalk with the help of two receive locations using two different pipelines that you wanted to use in the first place.
Puneet