Are you using the version distributed via Fidesmo or did you compile the applet from source?
Then, the curve your ECC key uses (ed25519) is not supported by the applet. Only NIST-P and Brainpool curves are.
As for RSA, Ill try to reproduce your issue. I had occasional problems when the wireless connection wasnt rock solid, the PGP process just fails if the connection is flaky sometimes.
The command ´./smartpgp-cli switch-p256´ works for me for example on a fresh applet installation.