Here's a step by step guide, I'm sure its a small thing you missed, but projection should not matter.
1) Have shapefile and bring into Geodatabase (SDE)
2) Right Click > Add Global IDs, also Register as Versioned (if you want to edit feature in ArcMap)
3) Create an mxd with your Feature Class
4) Double click on the data frame, Data Frame tab > set your extents, I personally click on "Other" > Specify Exten > Ok > Ok > Save mxd
5) Open ArcCatalog > right click on ur mxd > Public to ArcGIS Server > Put checkmark for Mobile Access
6) Open Mobile Project Center > Add Layers (Operational) > Find your service > Add
Hopefully one of these steps is something you missed, if not, please tell us what you did, step by step so we can determine if there's something wrong with your procedure.
Thanks,
Akhil P.