What are your system specs? I'm thinking that you might have a bad combination of using new software on an older system, seeing as you've upgraded cubase and windows but not your pc. Things will always slow down when this happens. You could try disabling a few windows 7 features and background processes when using cubase, to free up some resources. I'm just guessing tho as i don't know your system specs, but that latency is crazy high. Mines on 128 samples.
Theres a free tool called dpc latency checker, if you run it it'll show your systems performance. Any red spikes will cause buffer overloads.
Also in Cubase theres a setting to preload a bit of audio, might be worth trying this, see if it makes any difference.
Are you using the virus as an audio interface? Or do you have a dedicated interface?