An update on this...
I started seeing that the access to the problem file (rt.jar) returned to "normal times" since yesterday and the delay has vanished.
When I inquired the sysadmins, they mentioned that there was an anti-virus software running on those servers and it was doing the scan on access.
This was (most probably) causing the delay in open() system calls to that rt.jar file.
I am still not sure if there is a way (in Linux) to find out whether the anti-virus software was "holding up" the file access. The lsof did not return anything.
Unless you run the anti-virus software on the computer that is trying to access the file, I wonder how it can interfere with your access other than decreasing access performance similar to other users accessing the same file. Also considering that you mounted the filesystem directly from the SAN, how was the anti virus software accessing the file? Well, it seems the file was scanned for quite a long time.