I've occasionally had inconsistent flipper strength on Spike games where the EOS switch is intermittently registering (due to vibration). Meaning...if you go into switch test and can get the EOS switches to open and close rapidly (by banging on the playfield, or lifting a flipper up and then back down to rest) then that would result in occasionally weak flips. Really weak flips.
So it could be that, but doesn't sound like it.
So, the flippers don't get any stronger when you change the settings? Very strange.
Is it possible that the machine was assembled wrong, perhaps with the coil or the piece of the bracket that secures the coil opposite the coil stop were tightened at an angle, causing drag from the flipper plungers as they slide in and out of the coil? I would take a look at that area visually and make sure that everything is parallel or perpendicular, with no odd angles.
Move the flipper with your hand while watching under the playfield. Does it slide in and out cleanly?