You can have multiple, independent instances of the latest Feedback release, v 05.00.02. The prior release, v 04.04.03, did include feedback from all other Feedback modules on a site. Feedback v 05.00.02 when first installed does default to this legacy behavior but can easily be configured to limit the scope of a feedback module to its own submissions:
On the settings page for the Feedback module (the one which displays the submission form), open the section "Moderation and Feedback Management Settings". change the "Scope" setting from the default of "Legacy" to "Instance" and click update. Now, when opening the Feedback Moderation/Management page the admin user will be able to view, moderate, delete, etc. feedback from that particular module instance.
On the settings page for the Comments/Guest Book module (the one which displays published feedback), change the "Scope" setting from the default of "Portal" to "Selected Modules". A checkbox list of all feedback modules of the site will then appear. Check the module(s) whose feedback comments will be aggregated and displayed in this instance of the Comments/Guest Book.
Another way to separate feedback is to create a number of categories and assign one or more categories to each Feedback Module. Note that the Category List is shared by all Feedback modules of the portal. You could then have multiple Comment/Guest Book modules, each set to aggregate feedback submissions from all Feedback modules of the portal but displaying different categories of feedback.
Feedback version 05.00.02 is available for download from: http://dnnfeedback.codeplex.com/releases/view/50028
Note however, that this version requires a minimum DotNetNuke version of 5.02.03.