SimPE is only for Sims 2, so the fact that you don't have Sims 3 doesn't affect it in the slightest. It does sometimes have trouble figuring out what EP you have if you have a multi-pack, though.
Try a clean installation of it. The latest version didn't come with an installer, so you need to install it yourself. If you installed it to your old SimPE directory it had garbage left behind from the old version. Uninstall the old version, then delete the folder. Make a new folder and extract the new version into it. Then re-set the file associations to SimPE again by right clicking on them and adjusting the properties. (Unless you don't want them opening with SimPE for some reason.)
(By the way, I don't think this was a bug.)