Is there any benefit to having more than one link from the same site.
What I mean is would websiteA benefit from having a link on websiteb, pagea as well as websiteb, pageb?

Or, would Google penalise for this.

The reason I ask is that I have contact with a company who have arranged link exchanges with me in the past. This time they want me to do a 3 way link to a couple more of their sites, but in exchange they are only offering links on sites whose domain I already have links on.

Tricky. I'd assume it could look more like spamming, but I could be wrong...
Is there any way to negotiate having them link to other pages of yours?
Or are they adamant on linking the same page of your overall website?

I could see this being more helpful as apposed to penalizing if they link different pages of your website.

They would link to other pages, but I wondered if there was a problem because it is the same domain.

I strongly feel it would be alright as long as like you say, it's separate pages. But it's always a good idea to check around for other opinions and weigh out your options.

if the site website in question has a pr, it should matter that much

if exchanging links, see the blog that has a similar theme with the blogs that we have