Uhm, this is a long shot, but try a game with low file count.
In I've had a few games that took me 30-40 minutes to copy (I think Twisted Metal was one of them with like 16.000 files) and then others with few hundreds copy within 8-10 minutes.
If even the low file count files take long I can suggest can only suggest a simple copy test. Copy a file from HDD to the same HDD and measure time. Do the same for both the PS3 and external HDD.
It is quite possible that HDD is failing therefore slowing down the transfer speed, but it's pretty uncommon for stationary systems.