I got the same issue with a slightly different setup.
I have a master library in Aperture and I export various libraries for my family members. The exported libraries have the ".aplibrary" extension. Those libraries can't be synced with an iPhone or iPad via iTunes.
I am currently trying to see if I can get Aperture to export a ".photolibrary" file or change the contents of the Aperture library. From a inital look they look very similar but there is a few things missing in the Aperture library that I think iTunes needs to sync.
Anybdoy has similar issues or suggestions what could be tried?
When you sync an iPhone or iPad using iTunes you need to select whether to sync with Aperture or iPhoto. It won't do both at the same time. I know you are using iPhoto but since you actually have an Aperture library file you must select Aperture in iTunes. I'm not sure if iTunes only looks for an Aperture library to enable the Aperture sync setting or if it needs the Aperture app present.
With your device connected and selected in iTunes, select the Photos option at the top. There's a "Sync photos from:" menu with a popup. Select Aperture there. If you cannot select Aperture then another option is you could select to sync from a folder. To do that you create a folder in the Finder and export photos you want synced from iPhoto to the folder. This is a manual process that gives you more control over what gets synced but it's more work to maintain.
I don't know of a way to convert an Aperture library to an iPhoto library. You could just change the extension to .photolibrary but I don't know if that will cause other problems.
Try selecting Aperture as the sync from app in iTunes. I know when I quit Aperture it updates sharing information. So if you use iPhoto to edit the library I don't know if it updates the same sharing information.
As I think about this further, it probably won't work. iTunes only sees the last Aperture or iPhoto library opened. Since you haven't opened an Aperture library using Aperture, iTunes might not know what the last Aperture library is. I can't test this since I already have Aperture installed.
Thanks for the suggestions and yes I can see the selection in iTunes to switch between Aperture and iPhoto.
This works fine on my main iMac but unfortunately I have not installed Aperture on the other Macs in the house as the rest of the family is just using iPhoto. I just create the libraries on my iMac and move them out. So there is no option to select Aperture on the other Macs as it's not installed.
I know the solution is to install Aperture on the other Macs but I need to keep that environment as simple as possible as the rest of the family is not as computer literate as me and difficult setups immediately spike my todo list to help them do things.
I'll have to dig around a little longer but essentially it's not quiet correct that both libraries now share a common format. There seem to be still some historical fragments that prevent functions right across both formats.