I've been getting frustrated with my guitar lately because, despite how hard I try, I can't seem to get the intonation perfect. The tuner always reads it as being a little bit flat, and my saddles are as close to the nut as they can get. Any suggestions as to how to fix my problem? If it helps at all, I use 11 gauge strings, and have a Tune-O-Matic bridge.

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why don't you just turn your tuning pegs until the tuner reads "in tune" ?
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First off, afroboy, you don't know what he is talking about. I don't know how to solve your problem, take it into the shop and get a tech to take a look at it, you may have a warped neck. Maybe put up a picture of your bridge.
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What kind of tuner are you using? Intonation should really be set with a strobe tuner.
I'm gonna agree with Bean-o about the warped neck possibility.