Could you show us some reasonably short piece of code that reproduces the problem? Also, it would help to know what the program being called is doing, in particular the specifics of how it's handling reads and writes to the pipe. Smooth bidirectional communication depends as much on the behaviour of the process at the other end of the pipe, as it does depend on the side calling the open2.

For example, it could be some deadlock situation arising due to different buffer sizes involved, different timings, etc. (I.e. both sides are waiting for the other side to make the next step — which means that, without external intervention, they'd remain in that unfortunate state forever...). However, that's just a shot in the dark... I don't think there's any glaringly obvious explanation for why things are no longer working, so more details might help to generate other hypotheses.

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