Since I have plenty of ram (128GB) I thought it was weird that my VMs were kind of sluggish in terms of gui performance. I kicked up the minimum video ram to 1 GB using: "qvm-features dom0 gui-videoram-min 1024000". This made the gui a lot smoother in VMs, but upon reboot of qubes; sys-usb, sys-net, sys-firewall and sys-whonix were having trouble putting their respective icons in the tray. sys-usb in particular was not putting the "mouse popup" on the screen after booting unless I disconnected the usb hub my mouse was connected to and then re-connecting it. I tried setting the VMs minimum ram to a level above the 1GB minimum video ram (set to 2GB initial ram size) and everything started running smooth.