Hm, I followed the upgrade guide and I am sure I did not miss anything. The upgrade process finished successfully, I rebooted the vCenter host, updated vSphere client and vCenter version in vSphere is still 4.1.0 build 345043. According to release notes it is still 4.1 U1...
I really do not know what to do right now.. vpxd.exe Modified time is still 2011, when U1 was installed, so it did not change the file.
EDIT: Ok I re-upgraded vCenter, and now everythings is ok.