Aperture Not Recognizing Duplicates When Importing From iPhone. PhotoStream is Involved.

Question

Apple makes great software. Aperture is not some of it.
Here's my setup:
'11 MacBook Air OS X Lion
Aperture 3.2.2
iPhone 4 ios 5.0
1.5 TB External Drive. Aperture Masters and Library reside there, separate from each other.
I keep my photos in a structure such as: Aperture Masters > Year > Month > Date > original_photo_name
I'm running into trouble with Aperture not recognizing what photos are duplicates when it comes time to import photos. My workflow is that I'll import photos every so often, leaving them on the iPhone, and delete them twice a year.
ISSUE 1 (The Annoying One):
Aperture is showing a lot of photos that have already been imported even if I select "Don't Import Duplicates". Aperture has done this for a long time. I know that when it comes time to importing them, it doesn't import the duplicates, but this is just a sign that something doesn't work very well. (Maybe it's because I switched to an iPhone 4S and then back. I synced all my photos, and then back again to my iPhone 4, so the sequential number of the photos remained intact. I don't think that's the problem though.). This is just a minor annoyance that shows that Apple can suck at software (remember MobileMe?).
ISSUE 2 (The serious one):
short version: Some photos on my iPhone won't sync to my Aperture library because it thinks they've been synced through PhotoStream. They are not in my Aperture Library or in my Aperture Masters in the filesystem. How can I fix this. What bloody file do I have to delete for Aperture to stop being confused?
longer explanation: When iOS 5 came out, I was excited by PhotoStream. I had enabled it on my MBA, through iPhoto (I hadn't installed Aperture on it yet, as I was using an iMac to manage my Aperture Library). I believe it synced a bunch of photos from my iPhone, but then I stopped using it on my mac. Left it on on my iPhone. Installed Aperture. I initially enabled PhotoStream but swiftly disabled it once I was not sure how it would deal with photos being uploaded from my mac etc - just seemed like too much magic was going on. I then proceeded to sync my iPhone, not importing duplicates, and it synced a bunch of photos, but didn't sync some of them, displaying the following message:
Any tips on how to fix this and be able to import those images would be greatly appreciated.
P.S. - I thought that iPhoto might be causing the problem. I checked there and there were some images imported through PhotoStream, but not some of the ones which were not imported on Aperture. Putting that another way: the iPhoto library accounted for some of the images that were not imported, but not all of them. I deleted the iPhoto Library and tried reimporting with Aperture. Still no luck.

Answer 1

I have precisely the same problem. Very annoying. Worked fine with iPhoto, borked with Aperture 3.