The software supports that feature, but for it to work, the program has to be properly flagged as new.
As you've discovered, Verizon's guide data supplier (FYI Television) does not reliably flag new episodes as new episodes or repeats as repeats. Often, you will find new episodes flagged as repeats and repeats flagged as new episodes. The result is the feature to record only new episodes is not reliable. On many cable channels, it doesn't work at all; on the "big four" networks, it works, but only with a 60-80% success rate (varies by program).
On average, I missed several recordings per month with the FiOS DVR due to faulty guide information or improperly flagged shows. The best way to ensure that you get all new episodes is to record all new and repeat episodes, but then the Motorola DVR fills up quickly with lots of old episodes (and recordings get deleted due to limited space). Even that is no guarantee, though, because sometimes programs aren't listed at all, or programs listed are off by an hour -- this happens less frequently. Faulty guide data is probably the #1 complaint about FiOS service on this forum. You can read more information about this in dozens of different threads, but here are a few:
That and limited storage capacity are the main reasons why I bought a TivoHD for FiOS. TiVo gets their guide data from Tribune Media -- the most reliable guide data provider around. You can see a limited version of Tribune's guide data at Zap2It; TiVo receives a more comprehensive version.
At some point, Verizon will decide to address this complaint and they'll switch to a reliable operation like Tribune or Gemstar. When that happens, it will instantly upgrade the reliablility of every Motorola DVR in the field. Within few day or weeks, customer satisfaction will improve. But until then, you'll have to cope with it, buy a TivoHD, or switch providers.
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