The only difference between both links is the fragment identifier. That's why the page isn't reloading. The reason for this is RFC 3986 - Uniform Resource Identifier (URI): Generic Syntax (emphasis mine):
When a URI reference refers to a URI that is, aside from its fragment component (if any), identical to the base URI (Section 5.1), that reference is called a "same-document" reference.
[...]
When a same-document reference is dereferenced for a retrieval action, the target of that reference is defined to be within the same entity (representation, document, or message) as the reference; therefore, a dereference should not result in a new retrieval action.
You're fighting against the browser's correct behavior, and implicitly going against the user's expectations. I suggest you change the URLs to something like this:
www.mysite.com/shop/6-dresses?filter=[manufacturer:5]#filter=[manufacturer:5]
This will result in a reload of the page, without being dependent on JavaScript. Stack Overflow uses a similar approach for linking to answers:
stackoverflow.com/questions/3483627/some-question/3483650#3483650