Beside the programming issues: Modern OS and Hardware tries to guess what "might come next" so i also think the 2nd read is from cache also keep in mind that depending on the "clustersize" (i hope i got the right word cmiiw) of your filesystem there might also be already more read than just the very small portion of the file you might access (512 Byte is the minimum which is adressed by harddisk), maybe tuning your filesystem could also help.
Last but not least faster hardware could be an option: software raid is, surprisingly performance related not far behind (on modern systems) hardware-raid if you could spend the money, i/o is in most cases the bottleneck. I also wonder if one could hold some of the files (maybe the often accessed) in a ram-disk, but i got no experience if this is possible ...