If the problem persists after a change in theme, then it's obviously not the template files. There's a field in the wp_posts table that stores the number of comments listed against each post. WP uses this field to generate the displayed comment totals rather than recounting the comments every time (the latter would result in poorer performance). My guess is that this field wasn't updated correctly when you did the import. So, as I see it, you have 2 options:
1. Remove all references to comment_number() in the theme so that the "problem" isn't so obvious.
2. Manually fix the faulty comment totals in the database on a post-by-post basis.
Option 2 wouldn't be difficult if you used PhpMyAdmin (although I always recommend doing a backup before you edit anything in the database) - but it would be slow and pretty tedious.
Sorry I can't offer you anything more positive.