Czyli natywna. Próbowałeś systemowej? Na jakiej wersji testowałeś, bo w Alpha były chociażby:
[-] Fixed an AV when viewing some S/MIME certificates. [4.0.12.1]
[-] Access Violation: Send Email with attachment + IMAP + S/MIME
[-] TB 4.0.0.20 - Problem sending s/mime signed message - Access violation at address 00B7DFD5 in module 'thebat.exe'. Read of address 0000008C
[-] Signing an S/MIME message with attachments have caused an AV [4.0.7]
[-] (Alpha issue) Encryption in S/MIME internal implementation might not work [4.0.0.18]
[-] The Bat! was now able to display unknown certificate extensions when viewing a certificate by S/MIME internal implementation. [4.0.0.16]
[-] When signing a message using S/MIME internal implementation, or when exporting a private key, and the user has entered wrong pass phrase, no message was given. [4.0.0.15]
[+] You can now export multiple selected certificates at once to a single directory, when using S/MIME internal implementation. [4.0.0.13]
[-] When importing an S/MIME certificate (in the internal implementation) and you already had the same certificate already installed, and the existing certificate had a private key, this private key might have been lost [4.0.0.12]
[*] With S/MIME internal implementation, when you encrypt a message to a recipient that have multiple certificates and there is a certificate that gives an error and prevents from encrypting the message, you are now able to view this certificate by pressing "View Certificate" button in the error message box. [4.0.0.11]
[+] When verifying S/MIME digital signatures, The Bat! now shows time stamps made by a Time Stamping Authority (TSA) [4.0.0.8]
[-] When viewing a valid S/MIME signature, and it was singed by a certificate which was issued by an intermediary CA that was stored in the user's account, viewing this certificate did show "root not found" error.[4.0.0.7]
[-] The window to select a new name attribute in S/MIME (X.509) generation dialog was not centered on the screen; it was placed in the top left corner of the screen instead;[4.0.0.1]
[-] (#0006532) S/MIME decryption has caused access violations in 3.99.29[4.0.0.1]
[*] When a message is signed or encrypted by S/MIME or PGP or has a PGP key attached, a security button appears in the left top corner of the message text header. This button has a pop-up menu that explicitly shows the list of security actions available on this message (e.g. decrypt, show signature details, import certificate, etc). The most important action is marked by the bold font style. If you click the left mouse key on this security button, this important action is executed. If the message has more than one important action, the left mouse key then invokes the pop-up menu to give the user choice: which of the important actions to perform.[4.0.0.1]
[+] The Bat! now supports "Binary Signing Time Attribute" attribute when signing messages using S/MIME internal implementation. This attribute is defined in RFC4049.[4.0.0.1]
[-] (#0004146) On some S/MIME signed messages, the internal implementation rejects signatures as invalid due to "no signed attributes". The same signatures are shown as perfectly valid when verified with the MS Crypto API. [4.0.0.1]
[-] Export of S/MIME private keys to PFX files was incorrect[4.0.0.1]
Jak widać troszeczkę tego łatania było a i najnowsza wersja ma poprawkę odnoszącą się do S/MIME. Radziłbym przetestować najnowszą wersję i ewentualnie spróbować zmienić typ obsługi z natywnej na systemową, jeżeli natywna nie będzie właściwie funkcjonować. Ogólnie od wersji 4.0.0.20 nie powinno być problemów z wysyłaniem.