If I check my profile page I read "Total Down-Votes Received: 16", yet if I click the Posts Voted Down button, only one downvoted posts shows up.
My gut feeling tells me that it is related to my nickname change, because since then the downvoted posts list seems to give an inaccurate overview of the posts I was downvoted for.

The link to 'Posts Voted Down' are the list of posts that currently have a negative net vote count. For example, suppose a post receives two downvotes and three upvotes. The little number next to the post will have the net total, which is 1, and the post will actually be in the list of 'Posts Voted Up'. However, your member profile will count 2 against your total down-votes received.

Sorry for the confusion in the way the system is designed.

Before I changed my nickname the list showed more downvoted posts, I think it is too much of a coincidence to assume that exactly all of these were suddenly upvoted.
I'm not saying that it is impossible, but I think it is unlikely and that it perhaps requires some deeper investigation.

It's 200% not related to your username change.

However, was your username change around the time that we switched over to our new system (March 2012)?

I came back after a long time of inactivity, I changed my nick before March 2013 (not 2012), when I came back I was confronted with new features such as markdown syntax and endorsements, if these are part of the new system you are talking about, then I changed my nickname when the new system had been in production for some time already. Unfortunately I can't recall the exact date when I changed my nickname, I think it was the day after I had some talk with pritaeas on IRC.
I digged in the log files of my IRC client, but found out that they are circular, so that information seems to be gone on my part.

Our new system came out in March 2012. It looks like you just came back about 2-3 months ago. Welcome back :)

It looks like the change in the post votes list is related to the change in system. You just didn't realize it until you came back.

You just didn't realize it until you came back.

When I came back (new system being in production) I remember having observed a longer downvoted posts list, then after changing my nickname I observed that all these posts had suddenly dissappeared from that list.
If the new system is working correctly, then all these posts were upvoted after I changed my nickname, is there a way to confirm that?

If the new system is working correctly, then all these posts were upvoted after I changed my nickname, is there a way to confirm that?

Yes, but it involves digging deep into the database, and I'm rather busy right now working on another project.

I can confirm without a doubt, however, that username changes cannot affect anything like this since everything is tied to your user id, which doesn't change. Your username is entirely superficial.

This bug is already logged in this thread

I posted it in a separate thread because I wasn't sure as to whether the cause is the same.

well, if you check my profile, you'll see I have about 183 down votes (given by 30 members) ...
was one way that someone (no idea who it was) felt the need to search as much posts of mine (s)he could find and down-vote it.

when that 's noticed by other members, sometimes they check the post, to see whether or not the downvotes make sense, and, if not, they upvote to counter that downvoting. don't know, but maybe something like that may have had an influence?