Thank you very much for adding in the details! It's refreshing to see a question join.
To reduce it, shooting without flash has 2 additional stops due to the increase in ISO and ~ 1 additional stop due to the decrease in shutter speed. That's a total of 3 extra light stops!
The question now is: can your flash compensate for those 3 stops?
I think he can (note, I'm not familiar with his flash, but the guide number of what I can find is higher than my 430EX, which I think would cover the 3-stop gap in that room with ease).
What I think happened is a measurement problem. The window is causing a strong backlight, tricking the camera into thinking it needs to decrease the exposure. The flash is in TTL, which means that it receives the power instructions from the camera and from the camera's meter. I doubt it would explode with some power.
Now, what to do about it?
In strong scenes with backlighting, I think you should go to the full manual. Manual configuration of the camera and manual configuration of the flash. In this way, you completely control the amount of exposure you are giving to the backlit window and the amount of the interior.
If you do not use the manual and follow the TTL route, be sure to use a spot or center measurement and a meter from inside the room. By using the pattern measurement mode, I am pretty sure that the strong illuminated window caused the results you got. Why did the camera choose completely different exposures due to the flash? I have no idea, I just know that difficult lighting situations are the nightmare of automatic exposure modes.