Hm, not sure there is a short term solution to this.
3wire ports are now cleared to a default condition when a program exits, that’s currently digital input. Pneumatics are notorious for not handling valid control signals in a consistent way, it may have been that the power up condition (which was analog in) may have just been enough for them to turn off. We default the 3wire ports as a safety measure, we don’t know what the next program may be configured to do, and we also want to make sure any motors are disabled, using digital input is the de-facto way of achieving this type of thing.
Over the years we have had similar issues with pneumatics and other programming environments. see my detailed explanation of the root cause of problems with the cortex here.
We can consider adding something in 1.0.14 to mitigate this, but that may not be available before the end of this season. perhaps consider just creating a small program to set 3wire to digital output that you can run to keep the pistons activated or install an air valve.