I had an issue in a client project where I was signing a patch and when I applied the patch, the first dialog that came up looked like it hadn’t been signed. But, when I went to Programs and Features, clicked View Installed Updates and uninstalled the patch, the signature showed up in the first dialog.
I called InstallShield tech support about this and they confirmed it was a bug in InstallShield 2014. However, there is a workaround.
Go to the Direct Editor, select the ISPatchConfigurationProperty table, SignaturePassword property, and change the encrypted password to a plain-text version password.
Fixing the patch signing bug in InstallShield 2014
You may consider this workaround to not be ideal, because if you store IS projects in XML format, anyone could look in there and maybe see your certificate password in plain text (haven’t checked it though). But unless you distribute your project files, you should be safe until the IS 2014 service pack comes out.