I had a similar hiccuping problem on my 1998 E300D Turbodiesel. In the end it turned out to be a failing bit of the alternator that caused a torque transient load on the engine that eventually broke the belt tensioning feature. That cost me a new alternator and a new serpentine belt tensioner. But it was a weird problem - very much like a hiccup and at times it would do several jerks in a row and then just calmly go about its business. Eventually the alternator stopped keeping the battery charged and a big nasty red warning appeared on the dashboard and that was the way I discovered the problem. Before that I wrote it off as air in the lines that I could not identify a source for, and since it never stopped running or starting, I just kept driving.

Jim

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Own:
1986 Euro 190E 2.3-16 (291,000 miles),
1998 E300D TurboDiesel, 231,000 miles -purchased with 45,000,
1988 300E 5-speed 252,000 miles,
1983 240D 4-speed, purchased w/136,000, now with 222,000 miles.
2009 ML320CDI Bluetec, 89,000 miles

Owned:
1971 220D (250,000 miles plus, sold to father-in-law),
1975 240D (245,000 miles - died of body rot),
1991 350SD (176,560 miles, weakest Benz I have owned),
1999 C230 Sport (45,400 miles),
1982 240D (321,000 miles, put to sleep)