see my edited reply above for filename.
For other problematic file not worked any name change. Also copied the original name and uploaded a different file with exact same name, and it worked. But after editing the file (121 mbyte file became 120.1mb) its uploaded correctly 
There is some content-filname inferference
Some of these unknown problematic files can be uploaded with name change, some only with content change. I don't see any extreme with these, nor in size, or in name, so i have no clue why this bug happens.
Here is two of these files if you want to test, these are the ones that uploaded with short name, then renamed to the original name on the remote (server-side move), can't be uploaded directly with the original name: 8 MB file on MEGA
8 MB file on MEGA
did someone tried the test files, if the problem is reproducible?
I did actually. There is nothing unusual about these files. All works as expected.
Again - there is no known issue regarding crypt at the moment. Big part of rclone users (including myself) use crypt and nobody reported anything similar to your problem.
Of course there is always a chance of some new bug - nobody can be sure 100% but so far it looks for me that there is some problem with your configuration or remote - not with crypt nor rclone.
This thread already became a bit messy without you providing any clear evidence of any issue. I suggest you try to create reproducible case and provide all details for others to investigate.
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