The issue is the period. For some reason the RegEx is choking on that. You can get around it by escaping the period as follows:
<ModulePaths>
<Include>
<ModulePath>.*MyCompany\.Namespace\.Project\.dll$</ModulePath>
</Include>
<Exclude>
<ModulePath>.*ThirdParty\.Namespace\.Project\.dll$</ModulePath>
</Exclude>
</ModulePaths>
Also, the empty includes are valid and imply that all Modules are included. The comments of the Microsoft provided sample state that:
<!--
About include/exclude lists:
Empty "Include" clauses imply all; empty "Exclude" clauses imply none.
Each element in the list is a regular expression (ECMAScript syntax).
See http://msdn.microsoft.com/library/2k3te2cs.aspx.
An item must first match at least one entry in the include list to be included.
Included items must then not match any entries in the exclude list to remain included.
-->