I have a big problem with kanji words. I frequently make wrong, but close guesses at their readings!

For instance when I'm practicing my sentences in anki, I might get a sentence with the word 教室 (きょうしつ) but I may guess it as きゅうしつ and then find out that I was wrong. If I get words completely wrong, it's fairly easy to remember the mistake and learn the correct word... but I am finding that I KEEP making the same little mistakes over and over on words like this. Things like きゅ　きゅう　きょ　きょう　しゃ　しょ　しょう　etc... how can I keep these all straight when I am learning vocab?

Uhm, probably buildinf a foundation with familiar words like 教室 is a way to go.　Then moving to a little unfamiliar ones like: 家庭教師 and so on.

What we all learned with heisig stands for learning other stuff too. Building interconnection between words and sounds will make your memory stronger.

Is it possible that you're an auditory learner, and not a visual one? Do you pronounce the word to yourself while you're reading it?

I tend to make the same mistakes you do, but I knew I'd have trouble with it if I didn't hear it. To that end, I watch a -lot- of anime (and have been, since long before I started learning Japanese) and always say the word out loud, even if just under my breath. If I mistakenly say it wrong (reading too fast, misreading kana, etc) then I stop, clear my head , and repeat it 3-4 times the right way before I continue.

In addition, I tend to have the words run through my head all day after I've been practicing... This helps keep them right as well, though it's not a conscious thing... Kind of like a song stuck in your head. Problem words tend to get stuck like this more than non-problem ones, since I spent more time on them.

I hope this helps... And if you find anything else that helps, I hope you'll post about it on this board.

Just do more. You need more review is all. An saying it out aloud is very important. Your mouth muscles need their muscle memory trained as well.

Doing more repetitions is a way to go, but improving the quality of your input is vital. If you are learning pronuntiation, pick familiar sentences.

He isn't learning pronunciation, he's learning words.

It sounds to me like largely what wccrawford said. It seems like the sort of thing that would crop up by focusing too much on the writing of the reading rather than the sound of the reading, as きゅ　きゅう　きょ　きょう　しゃ　しょ　しょう etc as you list are somewhat visually confusing. You might try to focus more on the sounds themselves.

Of course, I use both extensively, because I'm a visual learner. At the end of the day the sound still plays the major role, though, because language is based primarily in sound.

I think I came up with a good idea to help. Right now, I'm only doing recognition cards. When I read the kanji and keep guessing the wrong answer to it, I think that keeps strengthening the connections with the wrong answer in my mind, and so that's why I keep missing it repeatedly. I think if I add some production cards for these same words (see the hiragana and produce the kanji), then that may fix the problem, as the wrong sounds wont have a chance to come into my thought process at all.
Repeatedly saying the correct phrase aloud sounds good too, so I'll do that as well.

I used to have the same problem. There are so many kanji with readings like きゅう　しゅう　しょう　こう　etc, I'd even start randomly guessing the most common ones.
That's one reason I used RTK2, and it fixed that problem.
Something that might also help is to learn several word that use the same reading. Like
教師　教室　教訓　教習 it's きょう　きょう　きょう　each time and that should help it stick.
Or you just need to practice your kana, if you're mixing up きゅう　and きょう because they look similar.

Anyway, one thing I've noticed is that the long vowel on-readings are more common than the short ones.