Without seeing your rig - I offer the following comment:
I have done a lot of hydraulic cylinders and these normally have a bone with a stretch-to constraint to move the piston into the cylinder whilst rotating both as they should - you could try just resetting the length of this bone in the stretch-to constraint. If this doesn’t work can you just make a blend file with the armature in it and attach it here so we can dissect it?
Normal practice for a hydraulic cylinder is a stretch-to constrained bone, I call it Stroke, with a stretch-to
constraint to an actuating bone called “Crank” (maybe even an extended bone of the actuator whose length is irrelevant, so stretch-to works easily). You then have connected bones on each end of the stoke bone to control piston and cylinder. I have found that if I alter anything on this rig - like scaling, rotating or moving the individual bones, I have to reset the rest bone length in the stretch-to constraint to get it to work again. Hope this helps.
Here’s a blend file with a sample “simple” hydraulic cylinder rig - rotate, scale or grab the Crank bone to see it work - then mess about with the bones in edit mode and see you have to reset length before it works properly again. If this is not the problem, sorry to waste your time!
cylinder-problem.blend (471 KB)
BTW you can achieve the same results by using empties and constraints rather than an armature - scaling problems then instantly disappear! Just parent the whole assembly (mesh and driver empties) to a master empty and simply scale this to scale the whole mesh/rig.
Here’s the solution with the empties and armature, you can do all the scaling,rotating and grabbing of the master empty you like and it will still work:
Just noticed I uploaded the wrong file - this is the one I wanted (just press Play to see it operate) Sorry! 
cylinder-problem-ver2.blend (714 KB)
Use the master-empty to affect the whole rig and the crank empty to operate the mechanism, use rotate, grab or scale on the master empty or grab and rotate on the crank empty.
This rig based upon empties is my preferred method.
PS. I have snap-to-grid enabled in this project (the magnet icon), to override this hold CTRL while moving, etc.
Here’s something with hydraulic cylinders all over the place that have to move with the whole model and still work properly even when the rig is moving over the ground: