Having played the Xbox version for a while now I will offer these tips.
Load saves from the space center, you will not get the correct save very often otherwise.
When you are starting to see weird behavior, cant click on items etc., go to the space center and then back to your ship and that clears those issues up most of the time. Occasionally you have to reboot but not often.
Do not keep to many save files. I try to keep it under 10.
It is a little buggy but I am enjoying the he double hockey sticks out of this game!