Somehow, it was. In my case, The reader omnikey 5427 did not work after a 
system reboot. Plugging and unplugging made it work fine again, until the next 
reboot. I found this reader creates a virtual net card and has a web interase 
for configuration/management. I captured the commands required for reboot, sent 
them with curl before my application startup and solved my problem. Perhaps 
your reader is similar. If so, you could program it to disable/enable the 
specific card type your having trouble with.
My case is on this list if you want more details. Right now - I don't have 
access to a computer 

-----Original Message-----
From: Santiago Gimeno <[email protected]>
Sender: "Pcsclite-muscle"
 <pcsclite-muscle-bounces+josealf=rocketmail....@lists.alioth.debian.org>
Date: Wed, 8 Oct 2014 13:10:16 
To: <[email protected]>; Talks about 
MUSCLE<[email protected]>
Reply-To: Talks about MUSCLE <[email protected]>
Subject: Re: [Pcsclite-muscle] Dynamically disable/enable specific card
        reader

Hello,

2014-10-08 13:01 GMT+02:00  <[email protected]>:
> Is the problematic reader the OmniKey?...
>
> I had a problem with an USB Omnikey. It din't work until it was replugged, 
> but it found a workaround.

Yes the problem is with the omnikey reader when it has a SLE4442 card
inserted. It hungs when the application sends an APDU with
SCardTransmit. I'm still trying to figure out why this happens, but in
the meantime disabling the reader seemed like an acceptable workaroud.
Was your problem similar?

Best regards,

Santi

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