This bug is probably due to you having increased your skills since the last time you beamed down to a planet. It happens to my BOffs' space skills too. Or at least it used to. Just be aware of that fact - whenever you spend skill points on one of your ground abilities, you may have to re-equip your tool bar when you start the mission. Luckily the game always seems to start you in a reasonably safe area so just get into the habit of checking your toolbar before you set off until they fix the bug. Consider it like an equipment check after beaming down - making sure all your kit was successfully transported!
It could be a client issue as I know I don't have the same bug and although they sound similar, mine were the BOff abilities, not the default weapon abilities. If it's a client issue, and you have some time (while the servers are offline!) maybe try reinstalling the game if you have your game discs handy. It might just be that some client file is missing or corrupted.