Yes, there was a change to the certificate handling in the 9.4.1 container.  It is possible for a single ".crt" file to contain multiple PEM blocks, each containing a different intermediate certificate.  Previously, only the first PEM block in a single file was processed, so that you had to use multiple ".crt" files for certificates with intermediate parts.  So this could potentially cause a problem if your ".crt" file has multiple blocks, but there's something wrong with one of the blocks.
I suggest it might be worth raising an IBM Support case if you need further help investigating.