How do I use a Savitzky Golay filter to find local maxima (in between samples) in a discretely sampled 1D signal?
While I'm not familiar with this specific type of filter, based on the plot you've shown, I would guess that the maxima that aren't found by your process are just butting up against the time resolution inherent in the process. Any kind of "smoothing" implies that there is some time-local smearing of the signal of interest, such that if there are two nearby peaks, it's possible that they will be coalesced into one. It's possible that a lower-order filter might present less of this behavior, likely at the expense of the amount of smoothing that you get.