We are using the Repository moule 3.1 and DNN version 5.1.

When we select URL option on the Repository module - the web browser (IE) thinks it is a pop up and blocks the external link from opening on some people's machines.

We would rather not have to give instructions to users to change their settings in order to allow this link from opening.
So, is there a way in which links to external webpages can open by default?
- afterall, it's just a simple link, but the browser thinks its a pop up.

our links are also encrypted (so the link looks like this: " _doPostback(....)"

the links are formatted that way (postback) so that the clicks can be counted and stored in the database for tracking.  javascript is then injected to to a window.open() to open the url in a new window.  Most browsers will treat that as a 'pop up'.  You can change the template.xml file to make the links open in the same window, which I believe will then do a simple redirect.  The downside is the new page will replace the current page in the user's browser, so they may navigate off your site.

If anyone has any suggestions, I am more than willing to make a change to the way links are handled.

btw, do you have the same issue with the Links module?  If you have a Links module on a page and add a link to a url and specify it to open in a new window, do you have the same issue?

edit the template.xml file for your repository template, find the [DOWNLOAD] Token, if it doesn't exist, create it.
Add a Setting named "target" and set it to "SELF" to open in the same window, or "NEW" (the default) to open it in a new window

<Object>
  <Token>[DOWNLOAD]</Token>
    <Settings>
        <Setting>
            <Name>target</Name>
           <Value>SELF</Value>
    </Settings>
</Object>