I haven't used Skip Peragus, so I don't know if it causes bugs. What I do know is that the TSL Restored Content mod does have some bugs in it which may cause the problem. I've used it twice, and both times the problem surfaced on Nar Shaddaa and the end-game sequence in the rebuilt Jedi Enclave on Dantooine. If you restart the game, try it without the Restored Content mod.
If you like, you can PM me your savegame. I can try to advance the plot using KSE's quest editor. Or you can do it yourself, but make sure to backup your game in case something goes wrong.