Analytics and AdWords - why don't they match?!

OK, I'm having some problems and can't figure this out.

A client of mine has an ecommerce site, has ads on Google AdWords and tracks conversion through both the AdWords system and Google Analytics.

Now, one would expect that figures for conversion between one and the other be different. This is due to the way they both work: cookies and suchlike (length of session, pressing stop and going back, etc etc).

Hence, Analytics becomes useless for my client - because they want to know what the real conversion figures are. So we turn to the AdWords Conversion system, thingy-bob that creates reports (i am sorry, cant be bothered to remember real names!).

So, supposedly, the AdWords reports would tell us everything from the cost of AdWords to the revenue earned. The revenue earned, in this case, would be created through the following piece of code:

!-- START OF Google Code for Purchase Conversion Page -->
<script language="JavaScript" type="text/javascript">
<!--
var comissions = 'x';
var google_conversion_id = 1xxxxxxxx88;
var google_conversion_language = "xx";
var google_conversion_format = "1";
var google_conversion_color = "000099";
var google_conversion_label = "Purchase";
if ( comissions )
var google_conversion_value = comissions;
//-->
</script>

So, as you can probably tell, the company makes money from comissions. Comissions for products vary according to the product. The comission is inserted dynamically as a template which includes the correct comission amount in the code.

Now, the problem: when I create a report, the majority of revenue appear as they should and correctly. However, a small minority, with no seemingly clear correlation, sometimes only show a revenue value of "1" (which is the default value but has been changed by the template dynamically. Obviously, this value of "1" messes up the revenue report and it's impossible to see the real conversion values....

Hope I was clear.. please help me out if you can

Cheers!

PS: I have just started for an online marketing agency and I will be participating a lot more in the coming future... so, hello!