Spotlight inconsistent -  files in Downloads folder and/or SeeAllResults

Hi
I'm currently assessing Punakea http://www.nudgenudge.eu/home, an app that allows one to tag files and stuff. It uses the comments field so in theory everything is still findable via Spotlight.
When tagging a file with Punakea one to choose to leave the file where it is, or to move it to Punakea's folder.
After much to-ing and fro-ing where I thought I was going mad, I have narrowed it to 6 test cases.
3 files in Download folder
- file A I manually added comment @AKK
- file B I used Punakea to add tag AKK and left file in place
- file C I used Punakea to add tag AKK and asked Punakea to move file
3 files in Mail Download folder
- file D I manually added comment @AKK
- file E I used Punakea to add tag AKK and left file in place
- file F I used Punakea to add tag AKK and asked Punakea to move file
A Punakea tag looks like this:###begintags###@AKK;###endtags###
(though there are some spaces up the front)
Then I searched in Spotlight for @AKK and it only found files A, D, E, F. Clearly Spotlight was treating the Downloads folder differently. I used the Spotlight preferences to first exclude that folder -- and file A stopped appearing. Then I removed the exclusion and, after some audible disk whirring, file B appeared.
So I thought I had fixed the problem, so tried another to match the file C case, and then noticed that file B had disappeared again.
I realised that I was on OS 10.5.2 so I upgraded to 10.5.4 and repeated the Spotlight preference changes, but got the same results.
For good measure, I removed Punakea's folder from Spotlight, and correclty file F dissappeared.
I then reinstated it, and I finally saw all 6 of the files listed. I clicked on Show all results and saw all 6. Came back to this post to keep typing - and then went back to check again - and now there's only 4 again - B and C have gone.
I must confess that throughout this whole test sometimes I have juts looked at the files in the Spotlight drop down, and other times I have used the 'See all results' - am now starting to consider that this is part of the issue, and so I need to repeat the whole exercise.
Throughout all of this Punakea found its files, B, C, E and F.
I suppose one workaround is to create a new Downloads folder for Firefox and use that instead.
There was a post to the Punakea forum http://www.nudgenudge.eu/support/spotlight-indexing-behavior which makes me realise I'm not the first person to fall down this particular rabbit hole.
Any comments ?
Cheers.

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          View ▹ Show View Options
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