I understand voting up the top reply, because it bubbles up and shows a count under the "Votes" Section.
Let's say someone's reply gets like 30000 votes, it will never make it's way to the "Votes" section and it will be overlooked and that awesome suggestion or idea will never be considered. This is unfortunate because it never got the attention it deserved from the right people and even though it got massive votes, it will go un-noticed to the key people that need to see the desire.
1) Perhaps the vote count should be Overall Votes not just the main topic starter.
2) Get rid of the votes on replies and turn that into a "Like" system and have a tab for "Most Liked"
This will foster votes to the top level, where they belong - and Likes for the suggestion within the post where they belong.
3) Or each reply in a thread that gets a vote, the parent also gets an automatic vote up.
4) Or something else...
The system just isn't working the way it is, something has to change.