I just started having a problem after upgrading from SF2 to 3 and using InDesign CS5. My exports to PDF were all crashing as soon as the PDF creation background process started. I tried all kinds of tests and troubleshooting to figure out what was causing the problem as it was sudden and erratic.
Then I noticed that all the documents crashing were using fonts I had activated with SF 3, so I created a new document with a simple system font and it exported OK. Then a font installed activated permanently via SF and still would crash.
I closed SF and reopen InDesign with a document using the SF permanently activated fonts, still would crash. It wasn't until I turned off SF3 Auto Activation in Preferences that the crashing ceased. I can now have SF3 open, activate fonts and see them in InDesign and export successfully without crash as long as that preference is unchecked.
This should be fixed in the next updated I hope as I like the auto activation feature.
Just posted as well on Extensis Forums:
http://forums.extensis.com/jforum/posts/list/3533.page