The issue is display-based only. By default, AE interprets DV resolution footage as Lower Field First. Because AE previews frames only (not fields) you end up only seeing one field during preview. This is only a preview issue, and shouldn't affect your output files, so long as you render interlaced output. If you still see the issue on output, you are probably rendering non-interlaced output.
You can turn field interpretation off during design work to see both fields, but remember to turn it back on before rendering interlaced output.