Yah very strange... so after discussing above a bit I threw together a sample project and this compiles fine against the 4.6.0 SDK I'm using, I can see the LineFormattedTarget class within my framework.swc when I expand it in the libraries in the navigator on the left:
<?xml version="1.0" encoding="utf-8"?>
<s:WindowedApplication xmlns:fx="http://ns.adobe.com/mxml/2009"
xmlns:s="library://ns.adobe.com/flex/spark"
xmlns:mx="library://ns.adobe.com/flex/mx"
creationComplete="windowedapplication1_creationCompleteHandler(event)">
<fx:Script>
<![CDATA[
import mx.core.mx_internal;
import mx.events.FlexEvent;
import mx.logging.targets.LineFormattedTarget;
protected function windowedapplication1_creationCompleteHandler(event:FlexEvent):void
{
var test:LineFormattedTarget = new LineFormattedTarget();
}
]]>
</fx:Script>
<fx:Declarations>
<!-- Place non-visual elements (e.g., services, value objects) here -->
</fx:Declarations>
</s:WindowedApplication>
I would check to make sure it shows the framework.swc inside of the 4.6 referenced library, if the swc isn't there try removing and re-adding the framework to the library path, if that fails with the same result I would look at pulling down the SDK fresh.