I had a similar problem a few months ago. The reason for me was, that whenever 
I used a too big response buffer for the card (400 something byte), the 
following commands behaved strangely, ultimately leading to a "Card not 
transacted" error.
I have no idea, if this applys to you as well, since I used a different setup 
(CardOS card and Omnikey reader), but maybe it helps.

cheers
Mathias

On Thursday 04 June 2009, Jan C. wrote:
> Hello,
> I have an Java Applet running on a Gemalto Cyberflex 64 card but in
>
> some operations I get this error:
> > Error code: -7fefffea (0x80100016)
> > Command failed: SCardTransmit(): 0x80100016, Transaction failed.
>
> The pcscd log says :
> >38127999 prothandler.c:130:PHSetProtocol() Attempting PTS to T=0
> >04367927 ifdwrapper.c:762:IFDTransmit() Card not transacted: 612
> >00000017 winscard.c:1637:SCardTransmit() Card not transacted: 0x80100016
>
> I've actually read this post in archive but I see no solution :
> http://www.mail-archive.com/[email protected]/msg06146.html
>
> Any ideas what's wrong ? I have linux 2.6.24-19 and  pcsc-lite 1.4.99
> with a Reader OmniKey 3111
>
> thanks,
> regards,
> Jan.
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