If your EFFECTIVE standings with the current agent are too low for you to pull a mission switch to another configured agent (if multiple are defined) or pause.

The standings it uses to determine if you can pull a mission are defined in your settings (but defaults are correct) http://wiki.eveonline.com/en/wiki/Agent#Access_to_Agents

<standingsNeededToAccessLevel1Agent>-11</standingsNeededToAccessLevel1Agent>
<standingsNeededToAccessLevel2Agent>1</standingsNeededToAccessLevel2Agent>
<standingsNeededToAccessLevel3Agent>3</standingsNeededToAccessLevel3Agent>
<standingsNeededToAccessLevel4Agent>5</standingsNeededToAccessLevel4Agent>
<standingsNeededToAccessLevel5Agent>7</standingsNeededToAccessLevel5Agent>