While doing in-circuit SPI flashing of several laptops for Coreboot, getting a good read or write was difficult. One of the many things I'd regularly try was to reseat the clip. Unfortunately, with the Pomona clips, this reseating would tend to catch and push in the pins of the clip, so they started making even poorer contact.
This pushing in was possible because there's not a single rigid pin straight through from the component to the test headers. The pin is 2 or 3 (I forget) parts, and a lower part can pop out of the plastic channel/groove it's in. You can disassemble the clip and push things back together, but it wasn't quite the same as before deformed.
I ended up having better luck with simpler clips that have a single physical pin straight through, such that the header pitch is the same as the component. Then I bent the pins to the side in an alternating pattern, to give enough room to attach my individual wires.