This might apply to things other than Writer - it's the only one I have had the 
opportunity to test.

If I create a new document in writer, I can create furigana (the proper name 
for these in Japanese) with no problems at all. 

However, if I load an MSWord .doc file that contains them, it messes up. They 
correct characters are displayed, but rather than appearing directly above the 
line they are attached to, they appear at a much greater distance. They 
actually overlap the main text of the previous line, which makes the whole 
thing quite hard to read.

Saving the file as an .ODT and then loading that file does not fix the issue. 
Whatever the problem is seems to be saved aswell. Adjusting fonts doesn't help. 

Cutting and pasting text between a properly working .odt and a broken .doc/.odt 
results in a variety of strange behaviors. .doc -> .odt often results in the 
spacing being fixed, but the furigana being the same size as the main 
line. .odt -> .doc often results in the text acquiring the defective spacing. 
unlike text originating in the .doc, however, if that text is cut&pasted back 
into a working .odt, it goes back to displaying properly. There seems to be 
some differances depending on whether it's being cut & pasted into an existing 
line, or onto a new line.

Unfortunately, so far as I've been able to tell, there is no manual way to 
change the spacing, and thus no way to fix it. Apparently, the pronunciation 
guide is considered "formatting" and is lost if text is selected, and "clear 
formatting" selected. This, incidentally, is moronic. Furigana are content, not 
format.