Sorry to gravedig, but I now have a similar problem - my (ID: 10351, Southeast Air Europe) average loadfactor in the last couple of hours seems to be at 99.99%, even though all my routes are at 100%. I know some of them are actually 99.66%, 99.84% etc. but doesn't average loadfactor function take data from the rounded up numbers you get when you go to 'View Routes'? If so, my average LF should be at 100%. I've added a couple of new routes, but the problem didn't disappear at any point.
Of course, it's not a big issue, really, but I can't say it doesn't bother me just a little bit. If you don't get it sorted out, it doesn't really matter. Thanks anyway.