My recommendation is to update your system to NI-Motion 6.1. We had a lot of trouble with the version you are using and there was a whole bunch of bugfixes for 5.1.1.
Please follow this link to download NI-Motion 6.1:
http://digital.ni.com/softlib.nsf/websearch/4405A2D094B3D6D386256DE300707983?opendocument&node=132060_US
I feel quite confident that your problems will be solved by the new version. Please let me know if you still run into the timeout issue after the update.
Regards,
Jochen Klier
Applications Engineering Group Leader
National Instruments Germany GmbH