Media Encoder won't import AVI MotionJPEG footage

I am trying to convert an AVI video clip to FLV format using the stand alone Adobe Media Encoder that comes with CS4. The AVI clip in question uses the codec Motion JPEG and Adobe Media Encoder refuses to add the AVI to the encoder queue.
This clip is the first of many that are being shot in classrooms using Canon Ixus still cameras which encode their video using Motion JPEG. The video needs to be FLV in order to be embedded in Acrobat 9 Pro PDF's
Any help with this would be appreciated.

I may have found a reason, at least for my specific situation, although I do not know if this fits anyone elses situation.  The video clips included in the After Effects project was an MOV file, created by a NewTek Tricaster video board setup.  In fact, this affected all my Adobe products (well the video related ones that is) because I ran into a bunch of issues getting them into AE in the first place, with the same difficulties in getting them into Premiere.  And the resulting project files (AE & Premiere) has huge issues getting into Media Encoder.  It was all stemming from these MOV files themselves.
I had to download a NewTek codec to even begin using them in the first place, and even with the downloaded codec, they are still hugely problematic to work with.  Unfortunately my company set up a great deal of time & money in setting these studios up, so I have to find a way to work with them.

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    Version 7.1.0 (141)
    Adobe Media Encoder CC
    Version 7.1.0.174 (64-bit)

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    My Adobe Media Encoder will not take mov. files! That should not be a problem, right? When I click the Add-button the mov. files is not listed up unless I choose to show all files. And when selecting the file, the program says the file could not be imported -_-
    Probably a stupid newbie mistake, but can anyone tell me what it is?
    I have downloaded the latest flash CS4 trial package, which include the encoder, and am trying to encode files provided with adobe's book "Adobe flash CS4 professional - Classroom in a book"

    I found the answer. I needed to install Quicktime lol

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    I'm using PPro CS4 on XP professional (German), Service Pack 3.
    From one moment to the next Media Encoder stopped working.
    When I try to export media from Premiere everything works fine until i start the encoding process.
    Media Encoder says "Loading project file..." (figuratively- i'm using the German version) and then freezes soon after ("application is not responding").
    I waited for more than 4 hours but nothing changes. XP's task manager shows that Media Encoder is consuming more and more virtual memory, but there ist absolutely no disk i/o.
    Media Encoder still works when encoding plain video files in contrast to sequences from premiere.
    What i did try up to now:
    - exported very simple sequences in different formats
    - reinstalled all Adobe CS4 Pro Applications
    - removed application data from user folder
    - installed the latest SATA/USB controller drivers
    but it still remains the same.
    Any help would be much appreciated!

    Hi
    Here is just one more unhappy Media Encoder user.
    Symptoms are the same described in this tread: ME freezes, nothing happen for 5 min. after hitting start queue. Then I get the following error  “Could not read from the source. Please check if it has moved or been deleted”
    I red almost all threads (and they are many) on ME troubleshooting. Didn't find a solution yet.
    In the C:/Documents & settings/.../Temp folder  there is only .prproj and epr (?) files that can't be red by ME.
    I tried different types of sequence to export in PPr including a simple .avi wide screen (and short ones too)
    I tried different output formats in Ppr exporting setting as well, including .avi, mpeg...
    I tried to manually add the .prprop file to ME and of course it didn't help
    I deleted the indexing of the folder (one of Harm or Bill's advice)
    I deleted the pref of PPr and ME  (see Genuine Project advice)
    I had no problem exporting to Encore and making DVD
    This is Win XP, PPr CS4
    I know I'm short with hw (laptop – 4 GB Ram) – graphic chipset and one hdd only and I'm looking for a replacement. But could this ME problem be a hw one?
    I keep hoping there is a way.

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