You're not alone in thinking this. When I was doing a little research on appendixes vs appendices there did seem to be a belief among many people that one form was correct for those things that give us appendicitis and the other form was correct for those sections at the end of a book. However, there seems to be no valid reason for believing this. If you want to use "appendices" as the plural of an appendix, then you use the same word whether it's bits of books or bits of bodies you're talking about.

There are plenty of medical texts that talk about "appendices" - e.g. (picked at random from a Google search): 
http://www.jmcreditorial.com/content/3/1/57

So I guess you just pays your money and takes your pick: appendixes or appendices.

For me, technical writing is mainly about getting the information across effectively. So, if most people find "appendixes" jarring and would expect to see "appendices", then I'll happily switch back to using "appendices". That doesn't mean one's right and the other's wrong. I just think that in technical writing (unlike in lots of other types of writing) the writing itself should be like good refereeing in a game of football, you shouldn't notice it - it should just be there in the background helping thing flow well.

I've always been more interested in making sure the content I was writing was understandable and correct than whether it met each and every criteria and rule of the English language (some of which contradict each other!).

This does seem to be a growing trend in technical writing, a move more towards the content than the writing skills, I wonder if it is because more of us are coming in from a "non-English literature" background than before? Not sure.