You need to run with -no-remote and a different profile for each instance. See https://developer.mozilla.org/En/Command_Line_Options
Thanks for the suggestion, which is helpful. However, it's not enough. Today, I had a hang, closed the debugging version, but the CPU was still maxed out. It was only after I closed the main version and all versions in TaskManager that the CPU load returned to normal. Despite the above precautions, there still seems to be some sort of interaction between the two windows, and this is highly undesirable. One of the aims of a good OS is to ensure that when one thread crashes, it doesn't bring down others as collateral, but however good the OS is, it's all for nothing if the programmers' of apps deliberately to share code between windows. For security and stability, seperate versions of an app running in different windows should be kept entirely apart.
Reporter, are you still seeing this issue with Firefox 3.6.13 or later in safe mode? If not, please close. These links can help you in your testing. http://support.mozilla.com/kb/Safe+Mode http://support.mozilla.com/kb/Managing+profiles You can also try to reproduce in Firefox 4 Beta 8 or later, there are many improvements in the new version, http://www.mozilla.com/en-US/firefox/all-beta.html
No reply, INCOMPLETE. Please retest with Firefox 3.6.13 or later and a new profile (http://support.mozilla.com/kb/Managing+profiles). If you continue to see this issue with the newest firefox and a new profile, then please comment on this bug.