After extracting the pixel values from the SMAP products, the resulted measurements file doesn’t contain data from all the file products and for every lat/lon coordinates. There is a file in hdf5 format for each day. It practically skips some of the files (days) completely or partially extracts for a few set of coordinates and not for all of them for the same day.
For example, I’ve added 10 SMAP Level 3 files (from 04.01.2015 to 04.10.2015). Using the Pixel Extraction function, I added the files at the Input/Output tab and the file with the station coordinates at the Parameters tab. The resulting 2 files (with measurements and product IdMap) only contain extracted data for 04.01, 04.04, 04.05, 04.07, 04.09 and even then, for 04.05, there is data extracted for only one station but there are 45 in total, each with its own lat/lon coordinates.
The toolbox is up to date
Example of a file - SMAP_L3_SM_P_20150401_R13080_001.h5
Windows 7 Pro x64
I’ve used the same file with station coordinates for extracting pixel values from SMOS L3 data and encountered no extraction problem.