For questions and problems with the CMS core. This board is NOT for any 3rd party modules, addons, PHP scripts or anything NOT distributed with the CMS made simple package itself.
I know this is marked solved but I wanted to say that this same exact thing has just happened to me. I was happily working along, customizing my mods and noticed I couldn't get some modules to work (captcha, uploads, etc). All investigation pointed to file permissions and I contacted my host. They changed up the permissions so that I owned all the files (have no idea why it would be otherwise) and now many of my modules have disappeared from the module manager. Others are showing installed but without an uninstall link. The files are there but not showing up in the module manager. AND I'm getting TONS of errors both on the site and the site admin.....some "headers already sent) but mostly "loadmodules" failed to open stream. I've removed whitespace and done all I can and its not working. Host says they didn't do anything but change permissions and that its a script issue. sigh.
I hate to reinstall but I'm nearing that. Hoping that tonight that something will be set right when the server reboots. Wondering if this maybe IS a script issue under this certain circumstance?????
I have no idea what caused this issue other than the host changing file permissions BUT I was able to delete the specific module directories via FTP that were missing in the module manager. And then simply download/install it again from the manager. Funny thing, some of my entries in those modules still appear. Just sharing in case others run into this.