Likely the cause: the M3 DS has an intermediate gear that is held down by a bent washer. The washer makes the first stroke 'stick' before the second stroke can be set in. The gear jams when the first stroke is complete, is released again for further progress when the second stroke is set in.
The gear is brass and I have seen three M3 DS's that had a tooth (or teeth) broken off the gear because on the end of the first stroke it jams on the teeth. The gear has to take too much stress if the first strokes are forceful and over time a tooth can break off.
Don Goldberg has the correct gear, but getting it in just right requires either a skilled tech or lotsa time. I never got it right on my first try, spent four hours figuring out correct assembly on my second... I heard from a fellow M3 DS owner that KEH's technical department eventually sent his M3 DS to Sherry Krauter at Golden Touch. A tech has to line up both connecting gears just correct before putting in the intermediate gear, or it will never work correctly...
OP is some time ago but I still hope this will help somebody someday!