Hi Garkonme,
For your equipment safety and reliability+availability, it depends. I would suggest you to decouple. If you think the alignment of others is ok. So you take them as a detum (subjected to your left one is moveable). Other than this you have to discouple and realign all the shafts...
Gaurdian,
Did you try this software alongwith the database of your system in another computer. Could be the problem of hardware support. Sometime it happen. Sometime the software does not support the hardware you are using. Or the OS (operating system). Try this may be it could help.
khan912