A couple of things I've found so far:
Selecting several instruments in the left-hand list (by shift-clicking on each one), and clicking 'Remove' leads to a list of anonymous things in the left-hand list where there ought to be the remaining instruments and buses. (I suspect a data structure got scribbled on by the remove code.)
The on-screen keyboard in each instrument seems entirely unresponsive when VE is invoked as a VST, which makes configuring keyswitches a tad impossible. (Works fine when invoked standalone.)
(Set-up: Cubase SX3, XP x64, EMU 0404 sound card; ask about what else you need to know.)
By the way, it might be worth creating a sticky thread for bug reports.