Within a word table row, it is possible to split up a cell into several rows and columns.
Word2MediaWikiPlus cannot convert this situation. The rows get messed up.
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This seems to work in version 1.0.0. It handles rowspan and colspan decently. Please report if you are still having this problem.
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I'm going to mark this one as fixed. Pretty sure split cells and columns work fine in version 1.0. At least, I can't find any cases where they don't work. Please reopen this if you still have this problem and report the version of Word you are using and the exact layout of the table you are trying to convert.