Hi,
Are you using multi-language in VirtueMart ?
Because if during the import you select the "wrong" language, HikaShop could retrieve the data from the incorrect language and give you a different result.
In your database, you can find one table per language for the categories and products (virtuemart_categories_..., virtuemart_products_...)
Regards,
Jerome - Obsidev.com
HikaMarket & HikaSerial developer / HikaShop core dev team.
Also helping the HikaShop support team when having some time or couldn't sleep.
By the way, do not send me private message, use the "contact us" form instead.