I have exactly the same problem and am using the 1.6. This is my original post in the Mod's thread:
Got a bug. I'm on Nar Shaddaa, finished what I need to do, got back to the ship and the whole place is in lock-down with no-one to be seen. The storage room is locked with no option to unlock it, as is HK's compartment. Also, for some reason I've had to fight Red Eclipse 3 times, although the 3rd time (this one) there is no-one on the Ebon Hawk bar my character. The first time had the original cut-scene, the 2nd one had Kreia taking out Bao-Dur and Visas in the cut-scene and that's it.
I 'gave' the Ebon Hawk back to that guy who approaches you saying he owned it, and this is my first planet.
Running Windows 7 64-bit and have the following Mods installed:
a reskin for the canon Jedi Exile
Bao-Dur's Charged Armor
Force Fashion 2
High Level Force Powers V2
Nar Shaddaa Backdrop
Prolog, Peragus, Harbinger Issues Fix
Coruscant Jedi Temple.