With no pictures, or the Nut or Bridge and saddle, its hard to advise you. The clearance of the bottom string at the FIRST fret could be as low as 1mm. Mine is just under a mm at the first fret. The 12th fret should be at least HALF of that 12, my 12th fret is between 3 and 4mm. There may be ways to lower the saddle (cutting deeper slots,) and you may be able to sand down the saddle, but without seeing it, there is no way to tell if that can be done. One other thing to check is the top of the guitar. It should be FLAT, no bulges behind the bridge and no dips in front of the bridge. Put a straight edge along the top from bottom to top and make sure its almost flat. Your top may look OK, but check it to be sure. Then make sure the neck is straight. Us at least a 20" ruler down the neck to check for any gaps bows or humps. Same size ruler for the top. Also measure across the top behind the bridge. If a straight edge won't lay flat along or across the top that might be part of the problem.
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