This sounds like it could be a compatibility issue with drivers/firmware and version of PDI.dll.
Can you write to
support@worldviz.com with the following:
1. firmware version: In piMgr go to help/about PiMgr and take a screen shot of the information displayed
2. driver versions
You're right, placing the sensors correctly during startup and when running the script is not related to the connection but hemisphere tracking.