Okay, looks like David was right. It was my misunderstanding of exactly how the two fields work together that cause his solution not to work for me.
In case this helps anyone else here is my solution and how it works:
First I had to hand craft the two fields as David had described...
<input <%
If category.Value = True Then
%> checked <%
End If
%> class="filterCheckbox" id="model_MarketCategories_<%=i%>__Value" name="model.MarketCategories[<%=i %>].Value" type="checkbox" value="true" />
<input name="model.MarketCategories[<%=i%>].Value" type="hidden" value="False" />
Now a quick recap of why there are 2 fields:
// Render an additional <input type="hidden".../> for checkboxes. This
// addresses scenarios where unchecked checkboxes are not sent in the request.
// Sending a hidden input makes it possible to know that the checkbox was present
// on the page when the request was submitted.
Now the reason both of the elements have the same name is this: If the browser will ignore all other input values with the same name once it has found one with a valid value. So if your browser always returns the value of the checkbox (regardless of whether it is checked or not) then the hidden element is ignored. If on the other hand your browser does not send the checkbox value if the checkbox is not checked, then the element immediately following the checkbox will set the value of the form property to false and return THAT.
My misunderstanding was that I thought the checkbox should always store the value of actual property, so something like:
<input <%
If category.Value = True Then
%> checked <%
End If
%> class="filterCheckbox" id="model_MarketCategories_<%=i%>__Value" name="model.MarketCategories[<%=i %>].Value" type="checkbox" value="<%=category.Value %>" />
This is what was causing issues... the checkbox 'value' should always be true. The hidden 'value' should always be false. And it is the state of the checkbox (checked or not) that will determine which gets returned to your controller.
Thanks David... sometimes the answer can be right in front of you but if your brain is not ready to receive, there's nothing a fellow programmer can do ;-)