Pathway currently has two problems/bugs related to Safari 3 (or rather, the other way around).
One is that when adding pages, no search results appear. Just type the right article title in the mean time, and hit “Add pages”, as a workaround.
The second is the malfunction of links on a page. Apparently, sometimes the underlying WebKit framework returns incomplete or bad information about the link clicked, and Pathway will not be able to follow that link. There’s no workaround for this.
The first one is fixed, but it’s no use updating Pathway since the second one is far worse and hasn’t been solved yet. There has been filed a bug report with Apple, and hopefully they will have fixed the bug asap.
In the mean time, I can only suggest you go back to Safari 2. Version 3 is only a beta, and I’m hearing some other apps have trouble with it too (mostly with a workaround or fix — I’m not that lucky here…)
Sorry for the inconvenience. I’ll have Pathway up and working again as soon as possible!