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To identify who or what is causing the problem you must do some tests.
1) the files of 11.6 MB is the same format as 34 MB. For example TIF, FITs or AVI ?
2) try to use only 3 or 4 files with 11.6 MB that seems to be the best frames. Choose them with visual analyse. Verify if the problem occurs.
3) try to reduce the size of 11.6 MB to 50%. Verify if the problem occurs.
4) try to use the automatic align points. Verify if the problem occurs.
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