Yes, that's right. Even if you don't get error messages, there's a chance that the other application depends on some changes made to the libraries that haven't been merged back into the our version of the Wixel SDK, so you should make sure you get those changes. You can look at the commit history on github.com, with TortoiseGit, or with the 'git log' command and this will let you see what changes slasi has made to the Wixel SDK.
If you want to have a single Wixel SDK that contains our latest changes as well as slasi's changes, you can install git and at the command line do something like:
git clone -o pololu git://github.com/pololu/wixel-sdk.git
git remote add slasi https://github.com/slasi/wixel-sdk.git
git pull slasi master
Please note that your merged Wixel SDK that this produces will not have been tested by either us or slasi, so it's more likely for there to be problems with it.
I should have noticed what was going on from the error message in your first post but in general it would help if you explicitly tell us what code you're trying to compile and where it came from, especially when the code came from a third party.