I review resumes for a living right now. So here's my take. I'm sure when they view your resume, they get the crappy cut and paste one. Since this is the format they ask you to submit it in, it probably does not lose you any points. I can also say that as someone who does this all day long, people spend way too much time worrying about what their resume looks like. The MOST important things on a resume are:
1.) The information that the reviewer wants should be very easy to find and read.
2.) Pretty much all other information should be omitted.
When your resume reformats itself, it may detract from the 1st criterion. To this end, instead of cutting and pasting, I would re-type the whole thing keeping in mind this first point. Also, since the topic of resumes came up, I'll give a couple of other tips.
-NEVER type paragraphs. Nobody reads them, and a reviewer is more likely to miss information that you wanted them to see becuase he will be skimming the paragraphs instead of reading them. Bullet points are much better.
-The resume is not an interview. Keep it concise, you are trying to get an interview, where an interviewer will ask for more information if needed. Keep it short and concise. (for aviation purposes this means ONE PAGE.) Don't include your job at Home Depot if it's going to take you to page 2.
-Last one.. Don't include references, or even mention that they're available upon request. We KNOW they are available. If we want them we'll ask for them. It just takes up room on your resume.
If anyone wants help with a resume, send a private msg, and I'd be happy to review it and give you my .02. I currently recruit faculty for a university. Not quite like reviewing pilot resumes, but I'm sure I share some resume pet peeves with pilot recruiters.