PrestaBay supports differents way to support ebay variation products.
It's send PrestaShop product with combination to ebay with variation option. For enabling this possibility it needs to activate option on Selling Profile -> Product tab http://screencast.com/t/JFC7R3IdUCYt
Send each PrestaShop product combination as a separate product to ebay. "Variation" option on Selling Profile should be disabled but on Selling list required to enable "Combination" option.
This look like this
1st - http://screencast.com/t/4KpAn6x8
2nd - select product from PrestaShop - http://screencast.com/t/rArWNeyE
3rd - you have selling list with each combination http://screencast.com/t/nxLgNcs5QK7
4th - result of list item
Send PrestaShop product with combinations as a single ebay listing without an options (variation). You need disable "Variation" option on Selling Profile -> Product tab. Also, does not enable "Combination" option on Selling List.