Encoding PP 5.5 clips in Media Encoder results in empty files

Question

I have several short clips that I send from PP 5.5 to the que in ME.
When I start the que in ME several of the clips (they are about 2 - 5 sec each) are encoded correctly, but some clips are just blanks.
The "ready" files are about half the size of what they should have been, and it looks like it is only the background thta has been encoded.
When I just go back to the timeline and do the procedure for exporting again, they normally encode fine - withot me having to do any changes in settings or else.
This is quite anoying - what could be wrong?
Reagrds,
Håkan

Answer 1

What version of Premiere Pro? Include the minor version number (e.g., Premiere Pro CS5.5 with the 5.5.2 update).
5.5.0
Have you installed the recent updates? (If not, you should. They fix a lot of problems.)
No updates avalible
What operating system? This should include specific minor version numbers, like "Mac OSX v10.6.8"---not just "Mac".
Windows 7
What kind(s) of source footage? When telling about your source footage, tell us about the codecs, not just the container types. For example, "H.264 in a .mov container", not just "QuickTime".
HDV MPEG
If you are getting error message(s), what is the full text of the error message(s)?
No error messages
What were you doing when the problem occurred?
Encoding the clip as said above
Has this ever worked before?
It works for several of the files, but some of them does not encode properly
What other software are you running?
None during editing and encoding
Do you have any third-party effects or codecs installed?
No
Are you using Mercury Playback Engine GPU Acceleration?
Yes
Does the problem only happen with your final output, with previews, or both?
Only final output. When clip is enoceded again, to replace the clip that did not encode, the encoding is ok, even if I did not do anychanges, just did it again