I also have this issue. I am playing a Bajorin Engineer. When i go on away missions, my weapon attacks are always missing. I have to manually add them every time. As you can imagine, this makes away mission pvp a dangerous thing.
Steps Ive take to try and fix this are that i have deleted the GamePrefs.pref file in the hopes that it would reset. But it did not. Also, having a problem with my space bar defaulting to one ability bar instead of the two i have it set to everytime i zone to a new map or instance.
Not really sure what else there is to do. I created a second character and the issue does not persist with the new character. I actually am starting to believe its a bug in the server side database for my character.