I had exactly the same problem with an Installshield 11 project which suddenly started exhibiting this behaviour for no readily apparent reason (I had used the "save as" dialog so that is probably implicated somewhere along the line). I absolutely could not resolve this in the UI despite trying the things mentioned on this thread (such as setting an resetting the subdirectory tick box within further "save as" dialog forms). Eventually I was able to track down a difference in the ism between the problem project and an earlier version which solved it. I had a line like this in the problem project:- ISPROJECTDIR1 and when I changed it to this:- ISPROJECTDIR11 the issue was cured. I have no idea what that table entry value of "1" corresponds to, or how to set it in the UI but it seems to cure the problem.
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