I was having a similar problem–I have been working with swf files in After Effects for a long time with no problems, but suddenly they came in as 72×72 black (same as others have reported).
Here is what solved the problem for me:
The swf files that were causing me problems were on an AVID ISIS server. Once I copied the swf to a different drive (any drive…internal HD, Internal RAID, external firewire, etc.–just not the ISIS), then the files imported into After Effects fine.