You may have too many layers in the drawing. AutoCAD drawings that have a large number of layer filters can affect system performance significantly. In some cases, you may not even be able to access the Layer Properties Manager. To remove layer filters from a drawing, use the FILTERS command. (See http://usa.autodesk.com/adsk/servlet/ps/dl/item?siteID=123112&id=8203173&linkID=9240617 for steps on how to do this.
The excess layer filters alert is controlled by the sysvar LAYERFILTERALERT.
0 Off
1 When the Layer Manager is opened, deletes all layer filters; no message is displayed
2 When the Layer Manager is opened, displays a message that states the problem, recommends deleting all filters, and offers a choice: "Do you want to delete all layer filters now?"
3 When the drawing is opened, displays a message that states the problem and offers to display a dialog box where you can choose which filters to delete
The default for the sysvar is 2 i.e. the alert will display only when the Layer Manager is open.
Hope this helps.
