I just posted this issue to the
official Uploadr 3 thread in the Flickr forums, but I never go over there unless I'm having a problem, and this one's so sneaky I'm surprised I even noticed.
I found a while ago that when uploading photos via the "Send to Flickr" shell extension, I wouldn't get an upload button. Easy enough, just relaunch the application and it shows up. But it looks like after Uploadr enters this state, all photos in that batch and all subsequent batches are uploaded with the sneaky "hide this photo from public searches" setting enabled, even though the default setting shows in the UI. Restart the application and launch the executable normally and the setting will behave as expected.
To see if this has happened to any of your photos, scroll down to the bottom of your photo page and click the "flag this photo" link to see if the checkbox is enabled.
There is discussion in the linked thread that there is a way to use the Organizr to change this setting for multiple photos at once, but I haven't been able to find it yet.
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