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Ok, I understand now.
Does this still happen if you are using the twentyeleven theme? Or only with your custom theme?
I think the default excerpt function normally does remove shortcodes using the WP function strip_shortcodes(). And MapPress tries to suppress maps in excerpts. But some themes use their own excerpt function and depending on how it’s coded MapPress can’t detect it.
In that case you must change your excerpt function to disable the ‘mappress’ shortcode.
You can ask the theme author about how to do this. Or you can usually find the custom excerpt function in the ‘functions.php. file and change it.
It depends on your theme, but there are also many suggestions about how to fix this problem on the web – for example: