Hi Katz, same problem here. As you said, when you use the Majestic query SEO Tools will get you only half of the domains. If you look them carefully you'll see that SEO Tool gets you the datas of the odd urls of your list.
So this is my temporary solution:
Extract the data for the odd urls, cut and paste them in a new Excel sheet, create a new ID colum and order the urls with odd numbers (1, 3, 5 and son on)
Get back to the first sheet, delete the first url from the url field in the Majestic Panel. Doing so the second all the pair urls will became odd urls.
Extract the data, cut and paste them in a new Excel sheet, create a new ID colum and order the urls with pair numbers (2, 4, 6 and son on)
Put all the collected datas in a single Excel sheet and sort the ID column in ascending order.
Done!
I know It's annoying but it works!
Have a nice day!