I am running OS X Snow Leopard with both Flash Builder 4.5 and Eclipse Indigo as separate installs. Flash Builder has completely taken over anything I associate with Eclipse. I do a lot of ColdFusion development. Sometimes I have to open single files from a system directory or over FTP (not in a project basically). 99% of the time I try to do this, Flash Builder opens instead of Eclipse.
Additionally, changing file associations never sticks. I will select the .cfc / .cfm file, open File Info, change the Open With dropdown to Eclipse (which I have to browse to manually each time and change the "Reccommended Applications" dropdown to "All Applications"), click "Change All", open the file and only sometimes it works. Regardless, the next file I open will be right back to Flash Builder.
Even crazier is sometimes I will choose Eclipse from the association dialog, press "Add", and Flash Builder shows up as the application I chose. It's maddening. No matter what I do, Flash Builder takes over.
The only solution I've found is to drag the entire Flash Builder application folder to the Trash, open the file I wanted, then (hopefully remember to) take it out of the Trash before I delete it by accident. It's ridiculous.
I've done lots of Googling and haven't found anyone else with this issue, but I imagine there is some config file sitting somewhere which is causing the system to think Eclipse is the same thing as Flash Builder.