I encountered a similar problem when exporting a gedcom file from Generations 8.5a to Legacy.
I found two possible workrounds.
1. Go to Options, Define Person Fields, Notes. Make sure the GEDCOM tag for your census info notes is set as NOTE. When you do the export, make sure the census info note checkbox is checked under the optional fields tab.
2. As an alternative, you could make a copy of your file before exporting and on the copy, before exporting, you could merge your census info and miscellaneous notes sections.
One of these techiques resulted in any initial 1's in the census info notes being stripped out but I don't recall which one. So if the census note should have started 1841 for example it ended up as 841. Cured on the imported file by a global search and replace .
Hope this helps - it worked for Legacy but am not familiar with Roots Magic. In any event, best experiment first with a copy of a subset of your file of course.