I'll try to elaborate here:
There are two sites in my network. One I work with on a daily basis (site A), and the other my colleagues maintain (site B), but I am a network admin. I can see the plugin pages for both sites. On the network plugin page and for site A, all of the newly installed plugins appear and are fully functional.
From the plugin page for site B, I do not see these new plugins installed. When I network activate plugins they only activate on site A. It's as if they're only installed on site A.
Furthermore, these sites also share the same theme with a different CSS stylesheet. The code updates I made in the theme template are reflected from the network admin end and on the front end for site A, but not on site B.
I'm thinking the problem has to do with the way I installed the updates, which I described above, but I can't figure where in the process the multisites would be left out. The plugins I'm working with are Co-authors plus 3.0.5, Term Management Tools, 1.1.2, and Export to text 2.4. The theme updates are in index.php and single.php. Thanks for the help.