Also, I found that uniuploader was failing for some mods (most notably ctraidassist). Turns out any mod/directory that has a read-only file causes the update to fail. To correct this, I wrote a new routine which strips the read-only tag off all the files and folders in the old mod directory.
As a reminder, if you have a zip file with /interface/addons/mod as the structure, you'll have to make a new zip with just /mod. However, this is much easier as you can zip up your own /interface/addons/mod directories in a batch with winrar and specify 'new archive for each folder', making the process MUCH easier.
1) get the uniuploader source and extract it
2) overwrite the Forms1.cs file with the Forms1.cs1 attached here (wont let me upload a *.cs file).
3) rebuild the project
C# Express is now a freebie, so $ is no excuse

Hope this helps someone other than me. We've been using it in our guild now and corrects some weird failures we had as well as making it easier on me to build packages. But, as always, no warranty/guarantee.