Are the form elements that are being populated from your client-side javascript set as disabled? If so, ASP.NET will ignore the value.
For example:
<asp:TextBox ID="TextBox1" Enabled="False" Runat="Server" />
<script type="text/javascript">
document.forms[0].elements["TextBox1"].style.disabled = false;
document.forms[0].elements["TextBox1"].value = "Value set from Javascript";
</script>
When this code runs, ASP.NET thinks that the textbox is disabled, and therefore discards its value in the postback, so the value of TextBox1.Text will always be blank. As far as I know, this behavior applies to all form elements. If ASP.NET thinks they are disabled, and they are subsquently enabled and populated client-side, the value won't be available on the postback.