Sorry to take so long. I saw a post about Google SketchUp and thought I would give it a try. Not Bad.
I would suspect n052 should be programmed for Fast Stop N.C. which would be n052=21 if E-Stop is connected to S3. It might be possible it was set to 4 for External Fault N.C. but that would require a reset after an E-Stop was pressed. There are plenty of possibilites, but these drives tend to be very reliable. Does the E-Stop normally require a reset? If so, I would suspect the E-stop switch itself or any other associated switches in series with it. You can check S3 with a meter or use u-06 to see what the drive reports. You'll need the manual to understand u-06. See page 4-3.
The manual is available as a PDF here:
http://www.yaskawa.com/site/dmdrive.nsf/link2_NewWindow/MNEN-5JLRKP/$file/TM.V7.01.pdf?OpenElement
If that is link is busted, search for TM.V7.01.pdf at
http://www.yaskawa.com
Mike Nash