Thank you for your post.
You see, the Store Manager does not allow to update the combinations while product import, and each time you proceed with import the combinations are being regenerated.
In order to regenerate product combinations correctly, you have to add all combination related columns to the .csv file like: reference, attributes, product images, price impact etc.
In case you will not add some of the details to the .csv file, they will not be included to products combinations after import.
We're planning to implement product combination update feature in further releases of the Store Manager for PrestaShop.
In order to speed-up the process, you're welcome to submit a request here: http://support.emagicone.com/823795-PrestaShop-Manager-Feature-Request