I'm not sure if this error is caused by a fault/different way of logging the flight-data when piksi is activated, or by the conversion of MP. Anyway, if someone has the same problem, you can use the sdlog2dump.py script from this site:
https://pixhawk.org/users/tutorials/matlab
As my logged .BIN file is a bit different to the example-file, I had to change the python-script in the following lines:
Line 62, add: "d": ("d", None),
Line287, change "time_msg = TIME" to: time_msg = None
Use this file with this command:
python sdlog2_dump.py Logfilename.BIN -f "export.csv" -d "," -n ""
The result is that all data (also the data of the piksi) is stored in a csv-file.