None of the recent updates have dealt with bookmarks or profile storage, and you can always copy or backup your profile at any time with the browser closed. I haven't had any other reports of FPR30 nuking bookmarks. Remember, if you switch back and forth to an older version of TenFourFox or Firefox, this can be an explanation, as the profile format changed with TenFourFox 45 (what eventually became FPR).
You can see if an old internal backup is present and if you see any bookmark files there, we may be able to help you recover from them (your profile folder is under your home folder in Library, Application Support, Firefox).
thanks for your prompt reply cameron,
i think you hit the nail on the head, an email link briefly opened a page with firefox, which must have caused the bookmark problem, would it be worthwhile deleting the firefox app from my machine?
The only reason I can think to keep Firefox 3.6 on your machine is because you have an add-on that won't work with TenFourFox that you must use. In that case, that's worth keeping it but you definitely should have separate profiles (if for no reason than to exclude the addon from TenFourFox). This is allowed and somewhat supported but not recommended.
If you don't have this requirement, Camino's final version 2.1.2 has the same renderer as 3.6 and won't interfere with TenFourFox.