Another vote for speedy stitcher and the waxed nylon thread they supply for sewing any caving gear (though I have no experience sewing knee pads specifically).
Out of interest, are the offending knee-pads the Velcro type, or the pull-up type?
I've never had an issue with stitching failing before wearing out the main pad, for the pull-up type. Sure, the seams get a bit tatty but never to the point of needing sewing before the pad is holed and ready for the bin (and that's with the warmtex coating too, for maximum life on the pad).
The Velcro type obviously have a lot less stretch, as only half of it is stretchy neoprene and the other half non-stretch webbing with Velcro, so they have a lot more strain on the stitching and obviously fail much quicker.