H264 movie stutters in QuickTime

I have a 1GHz G4, and h264 videos, e.g. movies, play fine in VLC player--perfectly smooth, but most stutter terribly in QT. I just updated from QT 7.0 to 7.6.4, with no improvement.
Clearly the system is fast enough to play such movies, at least up to e.g. 720x400. The problem is, the latest version of VLC Player for PPC/OS 10.4 Tiger won't play the latest h264 variants. All you see are the keyframes every 10 secs (or whatever)! QT 7.6.4 DOES play them, but it stutters and is totally unwatchable.
Are there any options to optimize playback in QT to fix this..? Or, can i perhaps somehow get VLC to use QT's h264 codec (that might not solve the problem if the decoder is what's slow). Thanks.

i did create a new file with the changes... that's how i know there is a difference.. the original works fine with not stuttering, but the edited file stutters... i did a total of 4 different files and all the edited ones stutter.
*Work Flow*
i just opened the file in quicktime, move the head to the location of the portion i wish to remove.. move the start and end thingys to select the portion i want to remove, press delete, repeat 'til all portions are removed.
don't have quicktime in front of me, but i think it's export.. save, saves as .MOV which stutters as well (tried that). export opens a dialog window.. chose MPEG4 in the combo box at the bottom of the window.. went to options and again don't have quicktime in front of me but they have an option for passthru for video and for audio chose that in both cases (could passthru be the problem? i've used it for audio before with no problem but not video).. change name.. export.

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Any idea why it would only just begin recently? I've never had a kernel panic until this past July, I just thought it might have been my new hardware.
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Thank you for your reply, Dave. I went to the link and went down the list to fill in information:
After Effects CC 2014.2, Version 13.2.0.49, All recent updates installed.
Quicktime Player 7.7.6 (1680.95.31)
Windows 7 Professional, SP 1
Xeon E5-2699v3 18-core x 2
64 GB RAM
64-bit OS
NVIDIA K5200 driver version 341.05
2 internal SSD and 1 internal RAID 0
No third party hardware
No other software running
No third party codecs
Render Multiple Frames Simultaneously is checked
Not using Ray-traced 3D renderer
Render Settings at Best, Full
Output Module:
Format: Quicktime
Video Output: RGB, Millions of Colors, Premultiplied (Matted)
Format Options: Codec: H.264, Quality 100
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Exact Error Message in AE:
After Effects error: Rendering error while writing to file:"<filepath>". An output module failed. The file may be damage or corrupted. (-1610153464)
Exact Error log in AME:
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12/24/2014 09:49:27 PM : Encoding Failed
Export Error
Error compiling movie.
Unknown error.
- Encoding Time: 00:00:00
12/24/2014 11:28:28 PM : Encoding Failed
Export Error
Error compiling movie.
Unknown error.
I'm able to render out the same file to other formats, such as Quicktime Animation, so no problem with the particular file. This problem is with all AE files.
Please let me know if anything is missing that would help. Thank you again.

I'm running snow leopard. The try to open any .mov file in Quicktime, and I get an error message that says, "The document xyz.mov could not be opened. The movie is not in a format that Quicktime player understands. I'm a recent upgrade to Snow Leopard.

I'm running snow leopard. The try to open any .mov file in Quicktime, and I get an error message that says, "The document xyz.mov could not be opened. The movie is not in a format that Quicktime player understands. I'm a recent upgrade to Snow Leopard.
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Unfortunately, the error message gives no details about what codec might be missing or what it needs.
If the file can't be opened in QT, it only means you cannot use the QT "Inspector" window to check what compression formats were used to create the file. It does not mean you can't use the Finder "Information" window to check on the compression formats or use a third party media information window (e.g., like VLC which will open many compression formats not supported natively by QT) to determine what kind of data is included in the MOV wrapper. If the file cannot be opened in any app, it is usually a good sign that the file itself is corrupted.
It's a stupid error message. Apple should do better than that.
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