We have a Java application which aims to generate digital signatures on
documents and transactions. The process for generating this signature is by
using our CSP MiniDriver for Windows 7. The problem is that at some point
these applications use calls to read from the Windows certificate repository
(using KeyStore.getInstance ("Windows-MY")).
For each certificate found, even if it is not necessary for the operation,
the application displays a popup stating that the item found is not required
for operation.

Assuming you have 5 or more certificates in the repository, and the read
operation is executed multiple times, and many popups are displayed, which
disrupts the operation. According to what was found, the access to the
Windows repository is done by the sunmscapi.dll library, which is installed
as part of the JRE.
This DLL sometimes would call the CryptAcquireCertificatePrivateKey()
function and this function would be displaying the popup.
Is there any way, from the Java application to hide the appearance of this
popup?

Could, for instance, the function be passed the CRYPT_ACQUIRE_SILENT_FLAG
flag?