Two Subscribe by Email versions after upgrade

Our site has been active for several years. It is a multiuser site with 5 active blogs. We want to upgrade from Subscribe by Email Version 1.0.1 to the current Version 3.5.3.

We attempted to do that automatically on the test version of our site from the WPMUDEV dashboard, but found we could not. Instead, we were advised that we’d need to manually download the 3.5.3 version and replace the existing Version 1.0.1. That version is a “Must Use” version.

We clicked the Changelog link on the Subscribe by Email plugin page, selected Version 3.5.3 for download, but instead of the download starting we were taken back to our profile page.

We then found that under the WordPress Network Admin Updates screen on our site there was an option to “Automatically upgrade” Subscribe by Email. We clicked that and received notice that the upgrade was successful. However…

Under our Network Admin plugins page, we now show Subscribe by Email Version 3.5.3 as “Network Activated”. Yet under the “Must Use” plugin category, we still show Subscribe by Email Version 1.0.1 installed.

Further we now have two links labelled “Subscriptions” in our blog admin menus. One (the old one) offers a link to “Settings” and a link to “Subscriptions” which is directed to [site root]/wp-admin/subscriptions.php. That file does not now exist on the server (if it ever did?)

The second (the new one) offers links to Subscribers, Add Subscribers, Settings, and Emails log. However, no Subscribers are found when we follow that link (http://[domain]/wp-admin/admin.php?page=sbe-subscribers).

We do have a table in the database, wp_##_subscriptions (where “##” is the blog id number) with some 1400+ subscribers; however, we cannot bring it up using either of these Subscriptions menus.

Could you offer us some direction as to how we might clear this confusion up?

Thanks for your help!