We may never know why. A cure is to create two 1099R with 1/2 of each and attach a statement explaining what was done. 

I posted https://proconnect.intuit.com/community/lacerte-tax-idea-exchange/mfj-mfs-split-of-1099r-in-communit... in the idea exchange. If you would like to see Lacerte do something like this then VOTE FOR THE IDEA