From your post I assume the Tersus Studio and Flex Builder are installed separately (in separate directories), and thus have sparate copies of eclipse, but somehow these installations interact.
My experience with multiple eclipse-based installations on the same machine is that they should function independently without having any adverse effect of one on the other.
The only point of interaction between separate eclipse installations is if they try to access the same workspace (not concurrently, as this is prohibited). If one eclipse copy accesses the workspace originally used by the other, the "worst" that can happen is that the specific perspective and/or one or more of the views that were used when the workspace was last closed (in the original eclipse) are not supported by the other copy - this may result in errors, but can be easily corrected by using the options in the Window menu to switch/reset perspective and open/close views.
I suggest you try the following:
I hope all this helps you in starting afresh. Please let us know either way (if there are complications, screenshots would be very useful).
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