So, you had a problem with multiple check boxes or choices for object merger. I am not sure you are aware of a hotfix posted by the developer on Wc3c.net. I am also not sure whether JNGP includes that hotfix already or not. Post #7 on http://www.wc3c.net/showthread.php?p=890931 contains the hotfix.
While the hotfix focuses on channel type abilities, it may have some bearing on other abilities.
Although the developer did not specify the actual changes to the tool, I suspect the changes have something to do with checkboxes.
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