Problem sharing .mov files to iTunes...

I'm making another attempt to solve a problem that's been vexing me for some time.  I have video files I've downloaded from the internet (legal content I have paid to download) that I can watch on my iMac using iTunes.  I bought an Apple TV (one of the first generation ones that has an internal hard drive), but only some of my video files will sync to it.
I've tried addressing the problem using the option in iTunes to create an Apple TV version of the file, but that failed (I got a message that said "Error occurred while converting the file "Filename". An unknown error occurred (-54).").  I get that message immediately.
I have Flip4Mac and Final Cut Studio (the version before the current version).  Since I couldn't fix the problem using iTunes, I thought I'd open the file with Quicktime and see if I could do something to convert it to something that iTunes could sync to my Apple TV.  So, I opened the file in Quicktime and tried to Share it to iTunes.  When I did that, there were three options:  iPhone & iPod, Apple TV, and Computer.  I could only select the iPhone & iPod option (the others were grayed out and not selectable).  so I clicked the Share button with the "iPhone & iPod" option selected.  An export progress window pops up, and it appears that the who export process is completed, but, at the end, it tells me "Can’t make file "Macintosh HD:private:var:folders:Ue:Ueqla9MhGcSWPlZdlCEsOE+++TI:-Tmp-:Filename (iPhone & iPod).m4v" into type alias."
This is all probably some basic aspect of how the video files I'm dealing with are created.  I'm hoping someone here can tell me, in fairly basic terms, what's going on here, and if there is anything I can do about it.
Here's some information about the file that might be relevant:  It's a QuickTime movie file (.mov), 135 MB, Codecs: AAC, Sorenson Video 3, Hint, 18 minutes, 2 audio channels, total bit rate: 961, Encoding software:  Sorenson Squeeze 5.0.
I'm a novice when it comes to video editing.  I really can't understand why in the world I have files that play in iTunes on my computer, but won't play on my Apple TV.  Is it a limitation of compatibility, or is it something that is done purposefully to the files?  How can I fix it?

Okay, I opened it with MPEG Streamclip and tried to export it in the Apple TV format three times, and every time I immediately got a message that Streamclip had closed unexpectedly.  It started to create the .m4v file, but only got about 8 KB into it, so it almost instantly failed.
I then used streamclip to export it to the .mp4 format, and that worked, which is very strange.  I would swear that I have tried that before and it didn't work.  Maybe I only tried to convert it to Apple TV format in the past.
You've helped me resolve an important issue, and I appreciate that.  Do you have any idea why the other options didn't work?
I'm going to set about converting some other files from different sources and see if it continues to work.  I'll post again then.  If everything goes well, I'll mark this thread answered.
Thank you for your help.
Note:  I should mention that these files are older.  They were created before the iPad was avaiable, and maybe before the iPhone and Apple TV (or at least early in the life of those devices).  They look like they may have even been filmed on video tape and converted to digital (they are not widescreen or HD).  I don't know if that matters or not, but thought I would mention it.

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