Does anyone else have this problem? Instead of overwriting my save occasionally it will create a new one even though it asks "Are you sure you want to overwite this save?".

Oops meant to put this in then regular Hardware/Software forum.

For me, it had to do with the savegames being 'read only' in the save game folder "documents/My Games/Skyrim"
when I ticked that off, overwriting did what it's supposed to.

This bug is caused by SKSE, i suppose you use SkyUI. Launch Skyrim without SKSE and you'll see that the saves will be overwritten.

I reported that nasty bug three weeks ago on the SKSE dedicated topic (http://www.gamesas.com/topic/1400450-wipz-skyrim-script-extender/page__view__findpost__p__21330874) but it seems that nobody cares...

Be aware that the pc game only accepts 2500 fresh saves (for the people that don't clean out their save games every so often).