It sounds like drive or file corruption. When running Media 100 under OS9, we used to get this message regularly after running speed disk to defragment our raids. We learned later that it is often better to simply delete (clear all its data to a low cost firewire drive FIRST!) and rebuild a raid. That was causing file corruption in the media 100 media.
Also, we experienced this type of message shortly before a drive hardware failure. It was so so very confusing because the clip would often play fine in quicktime player or import into After effects with no issues, but would NOT play from within the media100application. Sometimes opening the clip in quicktime player and "save as self-contained" would allow us to create a second copy of the clip that WOULD play. More often than not however, attempting this procedure would result in an error from within Quicktime player as well stating the file is damaged.
1) Check your drives with a good drive software program. (something better than Apple disk utility.)
2) Try copying the clip in question to another physical drive (ie. startup drive, or different RAID) and see if it plays.
3) Back up your data and reformat your RAID.
4) QUICKEST SOLUTION: just go ahead and redigitize the clip in question. If you continue to have problems after redigitizing this clip or if this problem emerges with other clips, I would suspect hard drive issues.