I noticed this behavior when working on my own alert action add-on, but I've confirmed it affects other add-ons as well so it seems like a Spunk bug.
1. Create an alert
2. Add an alert action, selecting one that has a custom UI. For example, the HipChat alert add-on.
3. Put some text in a text field (with the HipChat add-on, the "Room" field at the top works fine).
4. Save the alert.
5. Edit the alert again.
6. Delete the text from the field populated in step 3.
7. Save the alert again.
8. Edit the alert again.
The field whose contents were deleted in step 6 is still empty.
The field whose contents were deleted in step 6 contains the text inserted in step 3.
This is really undesirable -- Splunk folks, can you please log an internal incident and get some attention on this? See also splunk answer #386471, where I reported a related issue with how these fields get populated.