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I use both Pro-E & SW, and STEP is the best way to save a file for importing into Pro-E cleanly. Did you save as a STEP 203, and check the export options?
As a test, try performing a geometry check for slivers, or knife edges, and fix these using the direct editing tools (ex: delete face, etc.). If all else fails, try exporting as an IGES (check export options) and import back into SW (heal geometry if necessary). Then try saving as a STEP 203.
Pro-E WF 2.0 & 3.0
SolidWorks Office Premium 2007 & 2009