It sounds as though the XBMC installation is somehow still broken, despite the new install. When you clicked Uninstall, it didn't report any errors? Similarly, when you installed from that APK, no errors were displayed?
You could try installing the skin manually. Check if it is listed at http://forum.xbmc.org/forumdisplay.php?fid=67
and look for a download link for a Frodo compatible version (the latest of some skins are Gotham compatible, I'm not sure if they are backwards compatible). Follow their instructions, but normally it involves doing this: XBMC>Systems>Add-ons>Install From Zip> follow whatever steps they provide in the forum threads.
If that approach doesn't appeal to you, you could try a factory reset, assuming you're sure your iMX6 is a DroidBOX original purchased from us (as long as it was purchased after November or December last year, after a factory reset all apps will reinstall if you leave the device alone for twenty minutes). See this blog post for details - https://droidbox.co.uk/blog/how-to-access-your-droidboxs-recovery-menu/
you can safely ignore any warnings about our certificate not being issued by a known authority, or visit http://droidbox.co.uk/blog/how-to-access-your-droidboxs-recovery-menu/
once we get the http>https redirect issue sorted.
Once you're at the recovery menu, select (by using the Return Key on your remote) the Wipe Data/Factory reset option, then follow the instructions on screen. Once you've rebooted and completed any set up procedures offered, leave the iMX6 alone 20 minutes at the launcher's homescreen, without clicking on anything, you should then find all the apps are back again.