Blank input lines messing up sqlcl?

I have a bunch of .sql files created in SQL Developer, where they work fine. When I try to feed these to sqlcl, either on stdin or using @ /My/File.sql, ones with blank lines in them seem to be causing big problems; then blank line ends interpretation of the command as SQL and instead sqlcl starts reading them as commands. For example:

Error starting at line : 16 File @ /Users/a/lib/myfile.sql

In command -

FROM

Error report -

Unknown Command

Is this... expected? Is there a way around this in the tool itself? I can write myself a little pre-processor script, but to that point: is there some list of other differences I should be aware of when feeding SQL that works properly in SQL Developer into sqlcl?