I double checked, and I am on MS only.
I had a quick play indoors and was easily able to recreate it. Continuous shot, 9 point area focus, ISO 6400 (I think as it was set to Auto), Focus only shooting.
I focused the points on my relatively plain curtain and it occurred straight away but focussing on an object in front, in this case my tripod, it worked fine. So just wondering if it is getting confused when there isn't a 'definite' focus?
@Opteron: One thing which can mess up exposure in continuous mode is 'Shutter AE', which is on by default if I'm not mistaken. If you half press the shutter it will lock the exposure, which could be desired for single shot. Generally for continous mode it is not desired.
Thank you - I will check this out.
*EDIT* - I updated my camera settings and set Shutter AE to off and it still happens, almost every shot in a lowlight room (no chance to shoot outside during weekdays) this happened, though not always over exposed. Feeling a little disappointed tbh and hope Fuji can find and fix the issue in firmware