Round trip from Aperture to PS CS3 and back problem

Hi everyone; I hope someone can help me to solve this. I posted it before but the only suggestion I got was to check if the processed photo is not stacked under, which it isn't.
I have PS CS3 set as my external photo processing app (exports are PSD 16-bit 300 dpi) in Aperture 2.1.1. When I process the picture in CS3 and then save it(mind you I only SAVE, I do not do SAVE AS) as PSD (or TIFF) Aperture only shows me the original file in preview with the little circle informing me about the round trip to CS3. So the processed file does not show. Instead I only see two identical versions of the same photo or a layer from CS3.( I mean, I see the master and the version with the little circle).
If I save the work in PS CS3 as jpeg and then import into Aperture, it shows fine. When trying to import the processed and saved PSD and TIFF files, Aperture only shows the original file.
If it helps, I am working on layered pictures (HDR) where I use different parts of different pictures to get wide dynamic range. I export 3 or so photos from Aperture at once to CS3, process them into one, flatten the picture and save it.
And then Aperture just shows me the original file as version. I really need your help with this.
I have done this before 2.1.1 and it worked. Not sure if I have changed anything that might be causing this.
Thank you for your ideas.

Ernie, the photos are captured by Canon XTi so they are in CR2, saved to my internal HD and then "loaded" to Aperture as referenced files.
As for PS CS3, I am not sure whether I have it set up as a scratch disk or not (if you could let me know where to check it).
Yesterday, I did yet another round trip and found out that when I finish in PS and SAVE and CLOSE, then the file shows up properly in Aperture. What I was doing before was I SAVEd if but did not close. Then I would SAVE AS in PS to make sure I have some kind of a version of the file if the one in Aperture fails to work.
So it seems I cracked it but I would still like to hear what you have to say, or anyone for that matter. It seems to me that the SAVE-CLOSE is crucial.

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