Hi, I don't know if this is the exact same bug that I encountered, but it sounds similar in nature.  Where I saw it was after a scale change event and I wanted to toggle visibility.  The bug was introduced in ver 2.6 and is still in the 2.8 version.  I am told it has been fixed for the next release.
I had to add "navigationMode" to my map object:
var map = new esri.Map('mapDiv', {
        displayGraphicsOnPan: !dojo.isIE,
        lods: lods,
        extent: startExtent,
        slider: false,
        nav: true,
        navigationMode: 'classic', // Fixes an ESRI bug introduced at 2.6, toggling layers on/off at a scale change.
        logo: true
    });
Good luck,
Don