Probably because the second fetch of the page to get the combined script file ends up including Trace output. Probably workarounds: set CombineScriptsHandlerUrl OR CombineScripts=false.
Comments: Actually, to add to the confusion, I've just discovered that I get the same behaviour whatever value I use in the CombineScriptsHandlerUrl="MyScriptCombineHandler.ashx" property. I can see the page making a request to /MyScriptCombineHandler.ashx for the combined script, which dutifully gets returned, but it never hits the code in my handler, so something else is combining the scripts....
Comments: Actually, to add to the confusion, I've just discovered that I get the same behaviour whatever value I use in the CombineScriptsHandlerUrl="MyScriptCombineHandler.ashx" property. I can see the page making a request to /MyScriptCombineHandler.ashx for the combined script, which dutifully gets returned, but it never hits the code in my handler, so something else is combining the scripts....