Version 3.0.0 is two versions behind the latest. Do you experience this with the most recent release (3.1.1)?
Do your VDI connections use Blast, PCoIP, or RDP protocol to connect? When installing Duo, do you use the default option to add Duo to both remote and console logins, or have you enabled the “RDP Only” option?
I suggest you contact Duo Support directly to open a case as we probably need more information to troubleshoot this, like debug logging from your clients, etc.