There are two issues at play here, I think.
The first is a bug fixed here: on the back end, redirect nodes were letting the packet proceed straight forward in addition to bouncing a copy to the side. In many cases, this meant that valid solutions were being rejected. In others, it meant that solutions coincidentally took less time thanks to packets taking short cuts. This issue has been fixed.
The other issue is what @CuCN describes. If you go through the draft process to change a system, the solutions for the old version will get moved to the old version instead of sticking around. However, if you directly modify a system and provide the new solution as part of the same action, a new archival version is not created and old solutions stick around (harmlessly). @Melissa and I will talk to figure out if this is something we want to fix and how to do so. We might want a new version to be made regardless.
In any case, we’ll be removing the time rankings very soon. They were always a temporary feature, and as we get more players we want to make folks’ expectations more closely match our final intent. Player competition will take a different form in the final game.