if you are referring to the Taxonomy widget, I believe there is currently a known issue with filtering based on a custom module type for the built in taxonomy types (Category, Tag, etc).
Richard's suggestion of using a custom taxonomy type is a valid one. If you make a custom taxonomy type for exclusive use by your dynamic module, and set the taxonomy widget to use that type, it will work as you expect.
Gabe demonstrated this in the recent Module Builder Webinar
If, however, you want to use the built-in taxonomy types, a temporary workaround is to make a custom taxonomy control that inherits from the built-in one, and allows you to specify a dynamic type.
Simply add this class to your project:
DynamicModuleTaxonomyControl : TaxonomyControl
Type showcaseType = TypeResolutionService.ResolveType(DynamicModuleType);
.ContentType = showcaseType;
then register this control in your toolbox (specify the full type including namespace instead of the path to the control) and you will be able to specify the full Dynamic Module type and it should filter the tags based on that type.
Hope this is helfpul!