I've read from your post that you and your team have implemented HA on Linux, is it possible that the OSes of the two DS server have slight difference from one another? Example, 1st DS server OS: RHEL 4.7 AND 2nd DS server OS: RHEL 4.8.
According to IBM, having two systems at different releases is "not recommended". Their documentation expressly recommends "uniform configurations". They want the two systems to be exactly identical, mainly to make it easier to diagnose issues when they arise. I'm not certain that they'd refuse to support you, but they'd definitely be unhappy about the mismatch if you had issues.
With that said, I don't think Information Server cares as long as the version of DataStage on both boxes is identical. However, your HA software package (which monitors system "heartbeats" and does the failover if required) might require the O/S to be identical - you'd need to check with them as well.
However, I don't profess to be an HA expert, just someone that's configured or worked on some HA systems. If anyone else want's to chime in with more info that would be welcome.
Andy