The fault is with your source footage. It contains invalid GOP structures or other bad stream formatting associated with not 100% standard compliant MPEG derivatives. AE therefore cannotr reconstruct valid pixel datafor every frame. Try to convert the file externally in MPEGStreamclip, SUPER© or similar tools.
What version of After Effects? What is the codec used in the footage?
After Effects CS5 handles MPEG-based media (such as AVCHD files) much better than did previous versions.
I'm having a similar problem when importing an XDCAM EX1 movie file (exported from Final Cut) into CS5.
I may just export it to a different codec for the time being, but I worked with EX1 footage in CS4 without ever coming across this problem. Is there a specific update or codec that I need to download?
The Sequence settings from FCP:
Compressor: XDCAM EX 1080p30 (35mbs/vbr)
I checked the latest updates for AE and the software was up to date.
I did also try the link you sent to make sure, and the problem remains.