Hey dude, have you tried different gauge strings? I figure it could be a number of things but this may be a potential cheep fix.

You may also want to have a shufty round the old Guitar Tricks newsletter articles, I remember Azrael wrote one about well tempered tuning. You could also search for Buzz Feitin (sp?) tuning.

If none of the above work you may want to have a look at the acoustic intoneaters at stewmac.com