I am assuming you are using Core 3.7.1?
Open the attached version of jrefactor.e in a SlickEdit editor in Eclipse, and hit F12 (in CUA and most other emulations) to load. You should see 'Module(s) loaded' at the bottom of the editor. Now, does the described behavior persist? This should fix it. The problem happened in the 16.0.3 version of SlickEdit, which is the basis for SlickEdit Core 3.7.1, so the problem still occurs in the plugin. If you ever need to shut off 'Auto Organize Imports', you can find the options at Format > Imports > Options when a Java file is open.
Sorry for the trouble...let me know if you have additional issues with this.