Marc,
I suggest you read Thom Hogan's article about AF and TTL sensor maintenance. It is possible that your sensors got bumped out of alignment.
If the TTL sensor(s) is metering off a portion of the frame that is off the frame or in the wrong spot, then the flash exposure will be incorrect. So check out the article - and maybe it's time your camera took a trip to a Fuji service center. I know you do a lot of beach dives - that's I'm putting my money on that one.
If you're shooting macro in Aperture Priority, then chances are you camera is selecting 1/60th for your shutter speed. Unless you're in a REALLY bright location and you're setting your aperture at f16 or f22 then that's what you will get. The lowest shutterspeed the camera will allow with "regular" flash in 1/60th. For information, if you set the flash in slow or rear curtain sync, the exposure meters may choose MUCH slower shutterspeeds.
So another factor is that at 1/60th it just might not be possible to get to get good exposures under your conditions.
For macro where most or all of the frame is lit by flash I shoot in manual and set my shutterspeed at 1/125th.
Cheers
James