One possibility to consider is that an exception may be occurring in one of the lines preceding the confirmation dialog, preventing it from being shown.

For users of Internet Explorer, ensure that script debugging is turned on. Firefox users can install the Firebug add-on and activate it for the specific website.

If advanced tools are not available, a simple approach would be to insert alert statements after each code line to track down where the issue arises.

When working with JavaScript, it's important to properly reference your controls using the correct method. One way to do this is by using the following code:

document.getElementById(<%= txtInvNumber.ClientID %>).style.background = "yellow"

If you're still encountering issues, consider setting a breakpoint in your JavaScript code and stepping through it to pinpoint where the problem lies.

After running this test script in IE, Firefox, and Opera, everything seems to be working fine with the basic syntax. The issue might lie within the IDs or conflicting JavaScript on the page since it behaves as expected after 5 seconds. Without more information about the page, it's challenging to provide specific help.

<script language="javascript">
function lastCheckInv() {

    document.getElementById("test1").style.background = "yellow";
    document.getElementById("test1").focus();
    document.getElementById("test2").style.background = "yellow";
    document.getElementById("test3").style.background = "yellow";
    bRetVal = confirm("Are you sure?");

    return bRetVal;

}
</script>

<form method="get" onsubmit="return lastCheckInv();">
    <input id="test1" name="test1" value="Hello">
    <input id="test2" name="test2" value="Hi">
    <input id="test3" name="test3" value="Bye">
    <input type="submit" name="Save" value="Save">
</form>

Consider this: Could the .focus() call be causing your confirm to be hidden behind the page? Or maybe one of your control IDs is incorrect, causing the .style.background references to fail?

1. Make sure to set focus after displaying the confirm box, as otherwise the box will take away focus, rendering that line useless.
2. Avoid hard-coding ASP.Net IDs like that. Though they are usually consistent, a future version of ASP.net may not follow the same scheme, leading to complications when updating this code in the future. Utilize the server-side .ClientID property for the controls to insert these values into javascript as variables for easy reference.

Update:
As per your response to another comment, if the function returns true, this code will trigger a postback. In such case, there is no need to execute the .focus() line unless you intend to return false.

Directly accessing objects in JavaScript can sometimes lead to errors,

document.getElementById("ctl00_ContentPlaceHolderMain_INDet_lblFreight").style.background = "yellow"; 

To avoid potential issues, I recommend storing the object in a variable first:

var obj = document.getElementById("ctl00_ContentPlaceHolderMain_INDet_lblFreight");

if(obj)
{
    obj.style.background = "yellow";
}

If the object is not found in the DOM, it will prevent JavaScript from throwing an error.

Make sure to validate the existence of the elements before proceeding. Additionally, consider delaying the focus function until after confirming the action:

function checkInventory() {

    var elementsToCheck, returnValue;

    elementsToCheck = [
        "ctl00_ContentPlaceHolderMain_INDet_AddCharges",
        "ctl00_ContentPlaceHolderMain_INDet_lblFreight",
        "ctl00$ContentPlaceHolderMain$INDet$txtInvNumber"
    ];


    returnValue = confirm("Are you sure the information associated with this invoice is correct?");

    for (var i=0, j=elementsToCheck.length, element; i<j; i++){

        element=document.getElementById(elementsToCheck[i]);

        if (!element){
            // handle missing element
            continue;
        }

        else {

            // apply yellow background
            element.style.background = "yellow";

            // focus on the last element in the array

            if (i == (j-1) ){
                element.focus();
            }


        }

    }


    return returnValue;

}

function validateInvoiceDetails()

{    
   document.getElementById("ctl00_ContentPlaceHolderMain_INDet_txtInvNumber").style.background = "yellow";    
   document.getElementById("ctl00_ContentPlaceHolderMain_INDet_txtInvNumber").focus();    
   document.getElementById("ctl00_ContentPlaceHolderMain_INDet_AddCharges").style.background = "yellow";    
   document.getElementById("ctl00_ContentPlaceHolderMain_INDet_lblFreight").style.background = "yellow";    
   return confirm("Are you certain that the information linked to this invoice is accurate?");    
}

The initial two lines in your function contain errors, $ are not valid characters in an ASP.Net Control's UniqueID.

For client-side usage, make sure to use the ClientID and replace $ with _ .

If you are confident that the Controls exist, the provided code may function correctly.

Have you verified if bRetVal is defined in the code?

If not, using "var bRetVal = confirm...." serves as a clear indication to JavaScript that it should be treated as a variable.