T61 Ultrabay transfer speed question (again by the looks of the other threads)

Hello all,
I am scouting for the cheapest bang for my buck in the form of a +500Gb storage drive to slot in the Ultrabay. I did some transfer tests to see what I might need.
I formatted the WD 80Gb Scorpio that came with the lappy. Slotted that in Ultrabay and as expected it chugs along at ~50Mb/sec sustained.
At some time during swapping in and out PCM cards, SD cards, the Combo drive (you get the picture) I retested the WD80 in the Ultrabay. 15Mb/sec is what I got, I tried ATTO as it sometimes gives a clue. Sure enough after 40% of its runs the write/read stuck at 15Mb.
The usual desparado curiousity drove me to swap in the Combo drive and copy a file from that, 40Mb/sec, not bad. Also very confusing. Swapped the WD80 HDD back in and bingo its back to ~50Mb/sec on large file copies both ways.
I am a self taught dabbler with pooters so I can only make guesses and try to prove those guesses. A controller hardware or firmware bug? OS not happy with the hot swap format?
It ain`t the worlds end but like many of you I like to get the best out of my machines.
Its a 6457UG with a Crucial M4 boot running W7U, now with T9300 and 8Gb of RAM. Middleton BIOS and the SSD gave a works castoff machine a new lease of life. After 3 years of solid use I can say the machine does all the tasks very much faster than with the old WD80 Gb.