As WoW has evolved and the Armory has been updated, other tools have become available to circumvent these problems, and WoWJutsu (which does still bear the Beta banner) hasn't picked up on them yet. WoWJutsu's problems aren't neccessarily from poor design, however. It was a good design for when it launched. It was useful, and despite its inaccuracy, it was the best we had and the best we could do. The issue is that it simply hasn't kept up with the times. Better tools are available now, and WoWJutsu doesn't use them as well as other sites do. WoWJutsu was the pioneer, but others are taking the concept to the next level.
WoW's own Achievements single-handedly fix most of these issues- not only do achievements very clearly state whether someone has cleared a bit of content or not, it also comes with a date. Sure, there are oddities sometimes (like the mystery twink), but it's a far more accurate way of gauging progression. No worrying about logging out in the right gear or anything like that. Even if your armory profile fails to update for some reason, that issue can be corrected as soon as it does update. Your achievement is dated. It is a very efficient way for Blizzard to use it's own system to track progress, even if it isn't for overall ranking.
So what are some other alternatives to WoWJutsu? WoWProgress is a popular choice. In my experiences, it's much more accurate than WoWJutsu but still gets nailed with errors here and there. For one reason or another, a few servers are a huge mess and their progression ranking is out of order, but most of them are fine. WoWProgress also loses some points for its lack of aesthetic flair, but that might be a plus for some people- it's a very simple layout. The site also uses a scoring system rather than just a kill tracking system, so if you like that kind of thing, it's what you want.
A lot of people swear by WoWProgress, so I say give it a try.
My personal favorite is currently GuildOx. It doesn't seem like it has nearly the userbase that WoWJutsu and WoWProgress do, but I could be wrong on that. GuildOx lays out how it works very clearly on their About page, and though its rules are a little unfriendly to raid alliances, it's unlikely that you'll find a site that isn't. Raid alliances are very difficult to track, and they're sort of rare. I'm in one myself, but all of our allied guilds actually fit their rules just fine. We all have at least 20 members in our guilds, which is the bare minimum. Of course, this also futzes up the ranking system a little bit, but that's an issue that all similar sites run into. There's no escaping it with an automated ranking system.
That's my preference, but I have no doubt that some of you have suggestions of your own, and I'd be happy to hear them. I think the rest of the community would as well. At this point, I kind of want to call WoWJutsu the Thottbot of guild ranking sites. Sure, it was great when it was the first, but Wowhead and WoWDB totally blew it away and continue to do so. Hopefully WoWJutsu receives an overhaul and becomes among the best again, but right now it's best to look to the alternatives.