Hello Robert,
I don't know if this issue is still relevant for you. You are not wrong to expect this to work. Encrypted files should be architecture agnostic.
There have been a few known issues that can cause these symptoms. Links are below:
https://github.com/evpo/EncryptPad/issues/82
There can also be incompatibility between versions. Below is the quote from the download page:
"WAD format that is used for files encrypted with the persistent key file setting and double protection has changed. Files of this type that are larger than 64 kilobytes are not backward compatible and cannot be opened with 0.3.2.5. This does not apply to gpg and epd files with single encryption and without persistent key file."
I would appreciate if you provide more information to help investigate the issue: EncryptPad versions on both machines and which way the application was downloaded and installed on Ubuntu.
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Evgeny Pokhilko