The new drag and drop module sorting feature is breaking modules because it's adding that "sorting" feature to everything unnecessarily, and depending on when a user installs a module, the module may or may not even appear in the site because of it's placement in the installed list.
This happens with modules that are not using the same hooks for placement and are nowhere near related.
Example Module Number 1 uses a hook in the comment.tpl
Example Module Number 2 uses a hook in the header pligg.tpl
If a user installed Module number 1 before installing Module number 2, Module number 2 will not display in the site because it's placed in the list below Module number 1.
If you go into module management installed list and drag the module above the other one It will display module number 2 but then won't display module number 1 now.
Drag and Drop sorting should be either be limited to the sidebar, or a smarty variable needs to be created so a developer can wrap their code in it that will ignore the module sorting feature.
Rather than generically naming your examples, could you give me 2 module names that I could use as examples to try to reproduce this?