I have a project that is dependent on a custom list but the custom list is not part of the project. I then have a custom record that contains a multiple select field of the dependent custom list and I have imported the custom record instances. When I add dependency references to manifest I get something like

<object>customlist_mtg_secondary_class</object>

<object>scriptid=customlist_mtg_secondary_class.value_21_act#_481</object>

but this will not deploy. If I list the list values as object like so

<object>customlist_mtg_secondary_class</object>

<object>customlist_mtg_secondary_class.value_21_act#_481</object>

it does deploy any thoughts? I can correct the manifest manually but any subsequent use of the Add dependency references will remove my manual entries.

Looks proper without the scriptid= but I guess you are correct that you may have additional entries the next time you got Add Dependency References to Manifest. . .