Okay, I think I found the problem to why this was occurring.

When I was downloading modules and unpacking them, I would drill down to the folder that had all the files for the modules copy all the files, then go to the modules directory in xoops, make a folder and then paste all the files in there.

I would then go to the admin side to the modules section to install the module. Even on the ones from the new repository were doing this.

What I found, was that I was making folders named differently than they were in the package, and in those cases I would get the module not found error.

For instance, ZenCart for XOOPS when you unpack it has

Zen_Cart_Xoops_0.3_1.3 > modules > shop. Inside the shop folder is all the files for the module. I was going to my module directory in XOOPS and creating a folder called zencart. When I did this, I got the error. I deleted that folder, then just tried copying the folder 'shop' to the module directory. I no longer got the error Module Not Found.

Apparently the module is tied to that specific folder name as in ever case I created a folder with a different name than what was in the package, I got the error. Every time I copy the folder from the package to the module directory, the install worked without a hitch.

Hope this helps someone out.