This could be because your raster has a default band combination that is different from how you want the raster to appear. When you publish an image service I believe the service is published with this default display. If this is the case, you can create your own raster function template and publish the service to use this as the default dispaly template.
To create a raster function template open your imagery in ArcMap and set the band combination you want the imagery to use in the symbology tab of the layer properties. In the same tab, at the top right there is a save icon. Click this to save the band combination as a raster function template.
Now publish your image service. On the Service editor Window, select the Function tab under Parameters. Where it says manage raster functions click the Manage button. Add your raster function template file to the list and set it to the deafult on the drop down list at the bottom of the manage raster function templates window.
Select the rest of the settings you require for your image service as normal and publish your service. Hopefully now when you view your image service it will display using the raster function template you created in ArcMap.
