The system call API checksum doesn’t match
There was a lot of similar lines filling the console. I was a bit worried that the upgrade had gone wrong even though I had done three similar upgrades before this one with no errors - and that I would have to reinstall in stead.
Luckily, I found this error description in the 4.1 release notes stating that a reboot will fix the issue. So I waited for a while to be sure that the upgrade finished, rebooted, and everything looks fine:
Link to release notes:
"ESX service console displays error messages when upgrading from ESX 4.0 or ESX 4.1 to ESX 4.1 Update 1
When you upgrade from ESX 4.0 or ESX 4.1 release to ESX 4.1 Update 1, the service console might display error messages similar to the following:On the ESX 4.0 host: Error during version check: The system call API checksum doesn’t match"
On the ESX 4.1 host: Vmkctl & VMkernel Mismatch,Signature mismatch between Vmkctl & Vmkernel
You can ignore the messages.
Workaround: Reboot the ESX 4.1 Update 1 host. "