I'm still getting my query packets ready to go to agents and asked on a couple of writers' message boards about word count. I'd written my novel in WriteItNow software (WIN), which I like very well for the features it offers, but I exported the file to Word so my betas could make comments. I've been editing it in Word, using their comments, and because I have the entire novel as one file, so it's easy to do "find/replace" kind of things. Now that I'm pretty much finished with it, I put it back in WriteItNow so the program could print out my submssions in proper format (which is much easier than formatting them by hand!) Once I had that done - and I was SOOOOoooooo careful so I didn't copy more than one chapter into a file (each chapter is its own file on WIN), I did a word count and found it was WAY over what it should be according to the word counts done by Word! I went back and checked each chapter - only one chapter was in each file as far as I could tell. Argh. So I blamed the WIN software and growled and grumbled a LOT! Then I had to go through and reformat the novel to fit WIN's criteria (single-space, indented paragraphs, so it will print out in proper double-spaced format). As I went through the chapters clicking on the vast majority of the lines in each chapter, I finally found where an extra chapter had been included in one, thus messing up the word count! ARGH!!! But at least I found the problem!
In the meantime, I'd gone whining to the writers boards I frequent: Hatrack River Writers Workshop and Critters Newsgroups, and asked about word counts there. Everyone there told me "IT DOESN'T MATTER!" WHEW! They said if I was at 127,000+ words as WIN thought I was for a while, I should just say it was "complete at 120,000 words." What a relief! I actually have about 115,000 words in this novel, now that I can get a proper word count, so I'm under the 120,000 upper limit the agency sites say is acceptable for unpublished novelists.
Another thing I learned from these questions of mine on those message boards is that, if a paragraph or sentence breaks at the end of the fifth page, and the agent asked for five pages, it's considered unprofessional if you only send the five pages. Everything I've read said it was unprofessional to not follow the instructions, but as these writers said, common sense should prevail! So I'll include the sixth page that finishes the dramatic arc of the first chapter in just a few lines on that sixth page. Live and learn!