First, the correct way to do this is not with empty paragraphs, but by adding a Space Before or Space After value to the paragraph style. Edit the style, and all the paragraphs will change in unison.
That said, you cannot expect to align to a baseline grid if the space between paragraphs is not a multiple of the grid.
Yeah so I do usually use Space Before or Space After values – but on a baseline grid I am getting uneven columns if I have say 3 paragraphs in one column, and 4 in the other.
But that's a good point – expecting the baseline grid to absorb the difference in paragraph spacings isn't realistic. I guess I will just have to enjoy large gaps between paragraphs!
Thanks for the quick reply though Peter!
I'd just like to add for future reference if anyone has the same issue – that I had some luck with the 'Only Align First Line to Grid' option in Paragraph options. It mean's that your text isn't perfectly on the baseline grid at all times, but it means you can close the gaps between paragraphs and everything still lines up in the columns top and bottom.
Hopefully that helps someone!
Set your baseline grid value to half of what it is now.