I've been running into this issue since switching from Contribute CS4 to CS5. While at first I thought it was a fluke, it seems our other staff are now experiencing the same issue after they were upgraded. Here's an example of what's going on.
When a Publisher goes to create a new page from one of our templates, everything in the WYSIWYG editor appears to be fine. In our non-editable regions of the template, there are SSIs look like this:
<!--#include virtual="/site/example.html"-->
The above is correct, and when published (without the following problem) displays the header/footer/whatever just fine. But, sometimes after publishing, Contribute CS5 changes the code to be the following:
<!--#include ../directory/virtual="/site/example.html"-->
Where "../directory/" is a path on the server that I was currently at, but navigated away from to another directory (using "Choose Folder") in the Publish New Page dialogue box. So I was currently looking at the ../directory/ part of the site, but lets say I was trying to publish my new page in a folder called directory2 on the same level.
For whatever reason, Contribute decided during the publishing process that it needed to stick in that extra "../directory/" bit, which breaks the include and causes a "[an error occurred while processing this directive]" message to happen.
Is anyone familiar with this problem?