What version of SciDB and SciDB-py are you using? My first thought is that, in the most recent release of SciDB-Py, we fixed a bug related to toarray()
(discussed at http://www.scidb.org/forum/viewtopic.php?f=11&t=1392). If you are using a version of SciDB-Py before 14.7, you might be tripping over the same bug.
Can you check the output of
from scidbpy import version
And if the result is not older than 14.7, try updating (pip install --upgrade scidbpy)?
If that doesn't resolve your problem, then a data file would be helpful as well: