Word count: hyphenated words

There must be an answer somewhere in Absolute Write, but I couldn't locate it. Nor did I find a clear response from Googling. Is there an accepted rule in publishing about whether hyphenated words and phrases are counted as one word or multiple words? I refer to words such as pre-teen, which is not two linked words, as well as cat-lover, which is two linked words.

The writing program I use counts each part of a hypehnated word as a separate word, while MS Word counts any hyphenated word or phrase as a single word.

In the manuscript I just completed, there is a 3000-word difference between what my writing program reports on the cover page and what MS Word counts when I export it to Word format. That's a huge difference.

I don't know which word count to report. I know that magazine publishers always count hyphenated as single words, so they can pay the freelance writer for one word instead of two. But how do book publishers view this issue?

I'm trying to find a definitive answer before I start querying my masterpiece.

I suppose my concern is the thresholds that authors and agents often talk about. My manuscript is counted by my writing program as 90,500 words. It's possible that publishing professionals will immediately get the impression that a manuscript from a first-time memoirist of 90,000 words is a bit long, getting me off to a bad first impression. MS Word counts it as just under 87,000 words. Somehow being under 90,000 just comes across as less bloated. Naturally, I will submit it with the MS Word count. But I'm still trying to resolve in my mind what is supposedly correct.

I've done more checking, and the majority of comments seem to tip in favor of all hyphenated words counting as one word, but there's nothing definiticve. I didn't find any publisher's guidelines which say one way or the other on this issue.

By the way, MS Word also counts n-dashes with spaces around them as a word. Thus "Hello - there" is three words, but "hello-there" is one word. Weird.