You definitely don't want to lose the interaction the Nudge plugin gives you. That was just a test to see if the dataset had some issue that wouldn't allow it to be rotated (though I can't imagine what that could be). The functions for doing the actual rotations should be the same between the Nudge plugin and 3drotate. Is it possible you are showing a different sub-brick than the one you are rotating? The plugin shows a sub-brick selector to pick that sub-brick. For your anatomical datasets, there would be only a single sub-brick, but for the EPI data, you will have to choose the sub-brick in the AFNI GUI and the Nudge plugin to match. If that's not the problem, upload enough data for me to reproduce the problem, and I'll take a look.