I have the same problem. There a various "show-stopper"-alerts that disturb automatic image processing in photoshop. The only solution I found to use a little commandline tool called nircmd that has a function called "winwait". Basically you have to run it in a cron every X seconds and have it wait for a window with the title "Adobe Photoshop Extended CS4" and if that window pops up to automatically click "ok".
ugh a cron job.
There has to be some kind of real fix for this.
Pretty much once the file is opened I can handle any issue that would generate a pop up through code. Its just when I get pop ups when the file is opened.
please share, if you find a good solution. the cron was my desperate attempt (but keeps the service running for nearly 5 years now)
These dialogs are so annoying and I try to fix them as they er uh 'pop up' but some always get passed me. Is my test document just anything with a missing font? I'll check CS5 and see if it is still there.