Auto-sequences and reports displays reports via Report Viewer, which is an IIS application. It does this via an embedded Internet Explorer browser. If reports are not opening in-line and are instead opening in a separate Adobe Reader window, you will need to reset Internet Explorer.
Open Internet Explorer
Click settings (cog wheel top right under X button)
Click Internet Options
Click Advanced tab
Check 'Delete personal settings'
A reboot should not be necessary despite what the reset button says.