Let's bump this thread a bit. I'm suffering from the exact same dropoffs with my Seagate SATA2 7200.10 250GB drive. I got Vista Ultimate 64-bit installed on this drive and HDD access speed & time is totally random. Usually HDTach gives same kind of graph like ZappDogg linked above including sharp dropoffs and average read speed is 55-60MB/s. It gets even more weird, sometimes situation goes like this:
http://www.students.tut.fi/~koski7/pix/hdd_bench.png
Note the access time which is totally screwed. Also Vista experience index is showing HDD index of 4.1 instead of 5.7 which was the score 1.5 months ago when I installed Vista. Following changes have happened after Vista install which may have caused a problem:
1) I noticed IDE mode was Legacy IDE in BIOS, so I made some tricks and got ACHI working in Vista with no evident problems. Also installed Intel Matrix Storage drivers at this point. No problems, HDD index stays at 5.7. HDD access noise dropped somewhat with AHCI operation. However, I was not able to set write back caching or the other option (dun remember what it was) anymore in device manager for the drive. Event viewer says driver does not allow it (iastor.sys). MS' own ACHI SATA driver allows those options and shows drive working in UDMA6 mode instead of UDMA5 with Intel Matrix driver installed.
2) I noticed the drive still had 1.5Gb/s jumper limiter attached. I removed it. No problems in Vista, or at least I didn't notice anything drastical by the time. Matrix Storage console shows SATA2 operation as it should.
3) I installed 8800GTX to replace the GTS I had. At this point Vista asked me to refresh experience index which I did and HDD score was way off it should be. I had not paid much attention to index for a long time due to 4GB of memory helping lots in avoiding massive HDD usage and system was generally running fine.
Now I'm a bit clueless what is wrong in my system. I'm not very fond of reformatting my HDD for OS reinstall either. Seatools does not give any errors with long test. Drive is being properly cooled with temps varying in 36-40 Celcius range. Drive is attached to SATA1 port (Intel ICH7). I also have another Seagate PATA drive in my system which gives very nice consistent results with no weird dropoffs in HDtach whatsover.