When running mkvalidator on a file generated by mkvmerge 5.9.0 or later it issues the following warning:
WRN00C: Unknown element in CueTrackPositions [F0] at 20090944 (size 2 total 4)
What does it mean?
mkvalidator has encountered an element that it doesn't know about. This unknown element has the ID 0xF0 and is located as a child element of the well-known element CueTrackPositions at byte position 20090944. The size of its data portion (its "content", so to speak) is 2 bytes, while its total size (EBML ID + length field + data portion) is 4 bytes.
This can happen if mkvdalitor is run against a file that has been created with a mkvmerge version that already uses newer elements from the Matroska specs and mkvalidator has not been updated to match those specs yet. This is the case for the unknown element 0xF0 inside CueTrackPositions: looking at the Matroska specs we can see that 0xF0 is the new element CueRelativePosition. The same warning can be seen for the other new element 0xB2 which is CueDuration.
Update 2012-12-16: A new version of mkvalidator, 0.4.2, has been released which adds support for these two elements. However, it outputs other warnings about these elements; see the corresponding FAQ entry.
Another possibility of encountering this warning in general is that you're running mkvalidator against a damaged file and that it has found some garbage.