Was having the same problem. Just got off the phone with ATX customer service - we found a solution:
1.) In the business return go to the K1 form, next go to input.
2.) For the first shareholder use the COPY function to copy his identifying number (social/FEIN). Not cut, just copy
3.) While the identifying number is still highlighted press "restore" on the toolbar. Between Add Forms and Start Link. This should make the identifying number field go blank. Once blank, PASTE the number you copied back into the empty field.
4.) Save the return.
5.) Open the return you are trying to import the K1 into. Select Import Data, then K1 data and ATX should link the K1 to the corresponding return.
Customer support said you would need to do this to each K1 member. I've tried it and it has worked on 2 returns that weren't working prior to this fix. Also, in an effort to save time I've only done the fix to the first K1 and it seems to apply to all the shareholders. Again, have only tried it on a couple returns so not sure how effective this is...
Hope this helps