SSH-1.99-OpenSSH_4.1 vs. OpenSSH_3.8.1.p1

Are there any known issues with SSH-1.99-OpenSSH_4.1, as with version
SSH-1.99-OpenSSH_3.8.1.p1 I don't have to set keep alive parameter?

I am not sure if this is related, I have a ksh script that calls a db2 pl
stored procedure several times when it comes to certain iteration, it ends
up hanging in the middle. I experienced this with an environment that has
SSH-1.99-OpenSSH_4.1 but not with a different environment that has
OpenSSH_3.8.1.p1.

Thanks in advance