Q. With the new Version 2 software, can I run WinDR and also have Sys-Net control at the same time?

A. With the early releases of V2 software (V2.00, V2.01) this is not possible.
You would need to disconnect WinDR to enable Sys-Net control and vice-versa.

However V2.10 and later support the optional Sys-Net port, so that both can be run simultaneously.
You would need to ensure that the Sys-Net option has the latest firmware installed.