Which version of GeoEvent Processor are you using? If using 10.2.1, which method of "new" are you using in your feature service poll input, objectid or timestamp? If using objectid, look at the objectid values created by ArcMap and compare to those created by your Runtime app. When using the objectid option for determining what is 'new', GeoEvent Processor will only pull in items with a higher objectid value than at the time of the last poll. So if ArcMap was creating features with objectids of 400, 401, 402, etc... and then a Runtime app was creating features with objectids 10, 11, 12, etc... GeoEvent Processor will not consider the Runtime-created features as new since their objectid values are less than the features created by ArcMap.
At version 10.2, 'new' was determined solely by objectid, so all of this still applies (you just didn't have a choice to use timestamp). If you are using 10.2.1, and this objectid scenario is, in fact, what's going on, you have the option of using the timestamp option for determining what's "new". This option uses date/time values in an attribute field to determine what's new.
Hope this helps.
-Mark
