The "padding too short" check and error was removed from OpenSSL sometime
in September of 2006.
In particular:
http://cvs.openssl.org/rlog?f=openssl/crypto/rsa/rsa_eay.c
Version 1.52 of that file added the test which triggered this error report
and returned an error, and 1.53 removed it. That yours reports the error
in the error stack but doesn't actually return a verification error is
mysterious.
Interestingly, the time difference between those two versions was under 24
hours. The previous release was 0.9.8c a few weeks earlier, and it didn't
have the change either (obviously). I'd guess the version you're running
is 0.9.8c with that patch added manually, even though the patch was later
retracted by the OpenSSL maintainers.
I would guess then that upgrading to a newer version of the library would
remove the problem.
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