There are a few things you must first understand.
When you apply a change in FlashFXP (i.e. Click OK in Preferences) these settings are immediately saved to disk.
Now when the Preference dialog is opened it loads these settings from disk. FlashFXP will only update the internal settings for the majority of these settings if you click OK.
I felt this was the best way to manage multiple instances.
So for example
FTP 1 - you enable speed limiting
FTP 2 - if you open the preference dialog and click OK speed limiting will become enabled, and that's the only way.
There is an alternative option that you can add to the FlashFXP.ini, that will disable this type of behavior.
under [main] add
SaveOnExit=1
By setting this value, settings are not saved until exit, which means if you have two copies of FlashFXP open, make a change in FTP1 and exit, then exit FTP2, the changes you made in FTP1 would be overwrote with the from FTP2.
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