So ... mouse click problem not in MX 3 but in MX Pro? Is that what you are saying? We have come full circle, I think.
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Macro Express Pro v 4.0.1.1
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54. Fixed a bug where swapped mouse buttons didn't work correctly.
Let's assume for the moment that the above fix in 4.0.1.1 does indeed address the problem you had, and are having. I am not sure ISS means they fixed a conversion problem or they fixed an internal MX Pro problem. If it is a conversion problem, and you converted you MX3 macros prior to the above release, then maybe converting them again will resolve the issue.
If it not a conversion problem,and you are convinced that the mouse buttons are switched, then try the direct editor. Use its features to swap the click commands: <MOUSE RIGHT CLICK/> and <MOUSE LEFT CLICK/>.