I have just taken her to go see the elder(its the guy that replaced the first) and after their brief chat veronica turned round to me and just said come on were wasting our time. is that the wuest completed?

Unless it says quest completed, the quest is still active. You'll get a little surprise when you exit the bunker......

now whats happening is veronica is on constant alert and when she goes to speak to the eldar, he and his bodyguards go into alert and start running about the place

Veronica is IMO the most glitched companion. She punched a cave wall for 10 minutes while I was exploring. She goes on rampages with no hostiles present. I had to go back with Boone as soon as her quest was done. This is not the surprise (Veronica on high alert).

Oh, that surprise is: