This was happening to one of my pirates as well. A few of us here tried a couple of different things and this is what worked for me:

Make a new pirate. Do not accept any quests for gold so don't go to townspeople and defeat skeletons to recover a map, or fight ten crabs (EGADS!) for 20 gold.

All of the pirates that I built this way can enter doors. The two that I was doing the gold quests for could not enter.

the game is written in python and c++, i can't see how the java cache would have anything to do with it.

Just have fun how can It be boring your in a beta for a soon to be huge game I never got to lol :D

Thanks for all of the help but nothing so far is working:( So I am off to make a new pirate!

for me that cant be right, i've moved the mouse everywhere, i even drew my sword and i heard the change in the music but i just couldn't see the screen

It is the gold quests!
 

If you need gold play poker for it. At least you can continue to move in and out of buildings.

i tried making another pirate and it worked, i can enter buildings again except im less rich..... Thx Stella Ruby

Two of my four pirates cannot enter buildings. lol So what I've gathered from all this is that there is no fix?

Can't Get Into Bldgs.
 

As of the new release (1.0.6.0) I no longer get black screen, but I still can't get into buildings. The doors just open and close, and I'm left standing outside. Can't get "The 9 Rogues" from Elizabeth Swan in the Governor's mansion.

Good news:
New Logout button works; sort of...