It looks like the pulse is there but there is something corrupting the data only in binary form. Is there a setting that may not be correct?
Yes, but you have to recompile the oscilloscope application. Find following line in the source file DOFrame.cpp:
m_WFfd = open(filename.char_str(), O_RDWR | O_CREAT | O_TRUNC | O_TEXT, 0644);
and replace it with
m_WFfd = open(filename.char_str(), O_RDWR | O_CREAT | O_TRUNC | O_BINARY, 0644);
that fixes the problem. To compile the program, you need MS Visual C++ and you have to install the vxWidgets library. Let me know if you have any problem with that.
Anyhow I plan a major software update soon (weeks), which not only fixes this problem, but also reduces the noise considerably by doing a kind of two-fold calibration.