Not sure what to tell you.
I just created a UTM NAD27 zone 11N data set, points and polys (created polys as buffer from points). Defined both the data sets and the data frame in arcmap and published (to AGS 10.05).
Loaded into a OTB viewer and they display right where they should, and the points fall directly in the center of the polygons, so definatly no difference for polys vs points for me.
R_
(in my region, a SW/NE shift normally is the difference in NAD27 vs NAD83 UTM's.)
Just tried with AGS 10.11 and get the same results...