Currently (beta 89), there's a bug (?) where PIPE carrying particles overwrites them with BRMT when broken. I found this after trying to use it to store NEUT for bombs. It also happens with PQRT, and I only get some particles back when I try it with WATR. PIPE obviously can spawn particles that it's carrying, so why not make it do this when broken? I think it should spawn BRMT if empty, and whatever particle it's carrying if it has one.
Steps to reproduce and screenshots: http://imgur.com/a/1gyow
Agreed, I noticed this problem as well.