I've kind of been away from the scene for a while due to my computer dying, but the first thing I did when I got a new one was to install Sandboxie. One thing I liked about Sandboxie was how I could have disparate settings between browsers inside and outside the sandbox. Since I've installed I've noticed that if I have an unsandboxed Firefox open, when I try to open a sandboxed version, I get an error stating that firefox is already open. If I try to launch it again, it launches, but then says another program is trying to modify my window, and then tries to bring in whatever is installed on the unsandboxed firefox. Closing that window and relaunching nets the desired window - firefox running only the addons and containing the bookmarks used in the sandbox. I don't know if this is a known issue - I used to use Opera as my main browser and never had this problem on it. Any help would be greatly appreciated.

If I understand right, you have Firefox installed outside of any sandbox, and also Firefox installed inside of a sandbox.
This would be my interpretation of what might be happening ...
When you installed Firefox inside of the sandbox, the installer saw your existing Firefox program files and profile folders that are outside of the sandbox. It performed an update install, instead of a full install, because it saw that the program files were already installed.
And inside of the sandbox, it used the same Firefox profile name as the one that is used outside of the sandbox, and therefore assumed that the same extensions are already installed in the sandboxed Firefox.

So, both the sandboxed and unsandboxed Firefox are trying to access a profile folder with the same name, and if you start the unsandboxed Firefox first, it will create a "parent.lock" file in the profile folder that's outside of the sandbox.
The sandboxed Firefox will look for a profile folder with the same name when it starts, and it will see the "parent.lock" file that says Firefox is already running, in the profile folder that's outside of the sandbox.

After that, I'm not sure what behaviour might result. Maybe when you shut down the sandboxed Firefox it tries to delete the "parent.lock" file that is outside of the sandbox, but it can't so it may create a deleted "parent.lock" file inside of the sandbox. On the next start, the deleted "parent.lock" file inside the sandbox (which therefore hides the "parent.lock" file that is outside of the sandbox) will be overwritten inside the sandbox with new "parent.lock" file in the sandbox and sandboxed Firefox will start.

Anyway, you could try renaming the sandboxed Firefox profile folder, and edit the copy of "profiles.ini" that's also in the sandbox, but I've never tried that approach.
I always hide the unsandboxed Firefox profile files folder and Firefox program files folder, by temporarily renaming them, before I install Firefox inside of a sandbox. That way a full install will occur in the sandbox, and a different profile name will be used.
Then rename the folders outside of the sandbox, back to what they were.
I talked about it here:
http://sandboxie.com/phpbb/viewtopic.php?t=10785&start=5

Thanks for the help Guest10 - the sad thing is after I started reading you post, I remembered it. I just went in and created a new profile in each sandbox - problems gone. Thanks for the help and sorry for making you repost - my search was a inadequately performed it seems