which fixative regime are you using and which tissues are you having problems with? Some fixatives are better with certain tissues. For instance, picric acid-based fixatives (such as Bouin's) work fine with most tissues but are not recommended for kidney. I would have thought that the standard PFA+glutaraldehyde fix would be a good general fixative. Are you sure that your problem is not due to slow tissue penetration by the fixative? I assume that you are immersion fixing, in which case some tissues may be fixed later than others. Also glutaraldehyde doesn't penetrate tissue very fast which also may affect the preservation of morphology.
I don't work with zebrafish, but is it possible to dissect out the tissues of interest and drop them into fixative (perhaps you already do this)? If you have access to a suitable microwave, you could try microwave-assisted fixation which should speed up the process. Finally, what do other people use for zebrafish?
Not sure if the above helps much, but that's my 2cts worth.