uninstall both, and make sure you wipe both folders to make sure they are empty the default path for both that is unless you have done a custom install for either, clean the registry so no files are left over from the install of the game in question.
registry can be cleaned with any good cleaner, i use ccleaner but there's others to chose and it's safe as it only looks for dupes and left over files in the registry and repairs errors left over from installs and uninstalls / updates etc etc...
reinstall one game only, for me i'd choose the matrix version first and fully update it, once it's fully update and only then, redownload and install the steam version which will then update ok...
matrix inbuilt updater works fine, not got the steam version but same has happened before with other games so maybe same fix applies, won't hurt to try, only lose time as cost nothing
having 2 versions of the same game on the same pc / hard drive can cause problems updating, as the updater looks for the registry and install data to work, so either only updates one version or neither, but saying all this steam doesn't so i guess it depends on the install order, and thats why i chose matrix version first to bypass the steam one
please remember the advice i give / offer is member / player advice and not official support so might not be correct or work either and is offered as is, but is plain sense and meant to be helpful so good luck...
< Message edited by zakblood -- 8/23/2014 6:39:35 AM >