Go to the hanger section and click on the equipment tab. This will show you all the equipment you have on your ship at present. It's possible some glitch has caused equipment to be removed. If this is the case, simply drag it from display on the right to re-equip it to your ship. Make sure to check both configurations.
It certainly sounds like you may simply have some items not on your current configuration - I cannot speculate as to why.
Double-check your configs as described above, and if that does not correct the problem, then you should post in the Technical section with your User ID and server, so that the team can look at the issue in more detail. You should also make sure that you have cleared your caches, as recent updates may have glitched some settings.