are the verts from the same polygon?
nother thing, take into consideration the size of your model, is it huge? then you need a huge merge distance.
Try Snapping to verticies, then merge.
<html><font size=2>
<font color="blue">
And after calming me down with some orange slices and some fetal spooning,
E.T. revealed to me his singular purpose.
--TOOL, 10,000 Days---
</font></pre>
</html>