Your flash washes out the colors for two reasons. Direction, and Color. When you view the tank, you are seeing light that is reflected by the pigments from above the tank to you. If the light comes from the side, the pigments dont reflect much, if at all, because they are not used to having light from the side.
I used to have this problem with freshwater african cichlid photography. I used to breed tanganyikans, where many of the fish didnt have striking pigments so much as rainbows of iridescence. So a flash camera made it very hard to capture those colors. Until I started firing a remote flash from above the fish... then I got the cool colors.
The other problem is the flash color. Our eyes see in mostly green, then red, and then blue... only about 7% of our color receptors are dedicated to blue from what I remember... less than 10% I know for sure. So Lux meters, and white balance meters are based with a very low sensitivity to blue as well. So cameras have a hard time in the first place working with blue... very hard. Some are better than others, but you are pretty much into the $1000 range when you find ones that use the radiometric scale (full range, like a PAR meter) rather than the photometric scale (a scale that measures light with more attention to green and red like a Lux Meter). So many cheaper cameras, even those with 'white balance adjustment/metering' have a hard time adjusting for blue. Either the blue will be off, or the blue will be right, but then the exposure/speed will be too great or too little because then the camera has a hard time determining how much light is there.
And then, since most photography is done for our eyes, and above water, the flash color is mostly reds and greens, like a 6500K bulb or less. Not alot of blue there... so there go your colors, even if the camera gets it right.
The only way to get it right is to get a $1500+ digital SLR... they have accurate scales and manual overrides for all that crap if their better color sensors dont do it for you in the first place... but most do.