Take a look at the test file attached and the GIF with the steps.
1. All gradients have zero angle
2. Select All and call Transform Each dialog
3. Set an angle (I chose45°) and disable Transform Objects — this should rotate only the fill, not the paths. Apply.
4. Check the angles with the Gradient panel, the values is displayed as correct.
5. Create a new rectangle and set its appearance to the default one with D hotkey
6. Pick the Eyedropper toll and make sure both Appearance options are enabled in its options (otherwise it shouldn’t work at all: http://illustrator.uservoice.com/forums/601447/suggestions/37272676)
7. Pick the fill from a rectangle with the rotated fill.
8. The angle is not picked.

The problem seems to be similar to the one that happens with any script that tries to deal with rotated gradients... Script can read the parameter, but can’t write it. The common rotation method is used, and it gets written as a transformation matrix, I presume, and it is more generalized than just rotation, it can be anything likes skewing.
And Ai can’t automatically convert a simple one into the rotation.

Please address both issues.