Hi Raaj,
That is standard behaviour. In Reader the Highlight feature is turned on, which gives the light blue fill and the border highlight.
You can control some aspects of the highlight function using script, see here: http://assure.ly/jiZ6tn.
For example, the following JavaSript in the docReady event of the root node would turn off the highlighting:
app.runtimeHighlight = false;
Good luck,
Niall